From owner-chemistry@ccl.net Sun Nov 8 04:25:01 2009 From: "Green Power powergreen^-^gmail.com" To: CCL Subject: CCL: ONIOM calculations Message-Id: <-40632-091108042110-20275-j9VzQDQ0EKdLnWp51kBV4w^-^server.ccl.net> X-Original-From: Green Power Content-Type: multipart/alternative; boundary=000feaf48a7c2e6e720477d88690 Date: Sun, 8 Nov 2009 04:15:54 -0500 MIME-Version: 1.0 Sent to CCL by: Green Power [powergreen]![gmail.com] --000feaf48a7c2e6e720477d88690 Content-Type: text/plain; charset=ISO-8859-1 Dear All, Can I have a question about two layer ONIOM calculations. For a A(-)...B(+) system, I want to learn how the negtive charged A(-) is polarized by the positive charged B(+). I would like to know whether it is meaningfull to use the same theory levels, say B3LYP, for the two layers. This seems to me like a QM:QM model, instead of QM:MM which seems more meaningfull to me, Your valuable comments and suggestions are highly appriciated. Roy --000feaf48a7c2e6e720477d88690 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear All,

Can I have a question about two layer ONIOM calculations. = For a A(-)...B(+) system, I want to learn how the negtive charged A(-) is p= olarized by the positive charged B(+). I would like to know whether it is m= eaningfull to use the same theory levels, say B3LYP, for the two layers. Th= is seems to me like a QM:QM model, instead of QM:MM which seems more meanin= gfull to me, Your valuable comments and suggestions are highly appriciated.=

Roy
--000feaf48a7c2e6e720477d88690-- From owner-chemistry@ccl.net Sun Nov 8 07:44:01 2009 From: "Yang Mingjun jeffle07^^^163.com" To: CCL Subject: CCL: relax the docked complex Message-Id: <-40633-091106211042-1763-cMEl05BNbEglTkPpjWeE3g+/-server.ccl.net> X-Original-From: "Yang Mingjun" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Sat, 7 Nov 2009 09:25:14 +0800 Mime-Version: 1.0 Sent to CCL by: "Yang Mingjun" [jeffle07[a]163.com] Dear all, I am going to perform molecular dynamics simulations of protein-ligand complex, in which the ligand is placed into the binding pocket of the apo protein by docking methods. A few of the residues in the resulting complex around the ligand should be readjusted to interact properly with the ligand. However, there is not a guide of how these residues should be adjusted. I'd like to know how should I fix this problem? Is there any software or method for the job? Many thanks. Jeffrey From owner-chemistry@ccl.net Sun Nov 8 09:11:00 2009 From: "Serdar Badoglu sbadoglu++gazi.edu.tr" To: CCL Subject: CCL: linc & linp ? (SQM) Message-Id: <-40634-091108090004-13124-ZTFeaxj2ITJ434XfiGOpww!=!server.ccl.net> X-Original-From: "Serdar Badoglu" Date: Sun, 8 Nov 2009 09:00:01 -0500 Sent to CCL by: "Serdar Badoglu" [sbadoglu#gazi.edu.tr] Dear CCLers, I used to calculate the total energy distribution of normal modes of subject molecules in PQS-Chem's SQM package. In my last calculation I have seen two keywords which are new to me. They were the "linc" and "linp". In the documentation, these keywords are said to be "colinear bend" and "coplanar bend", respectively. But there's no further information. I'd like to know exactly what are the colinear bend and coplanar bend. Regards. Serdar Badoglu From owner-chemistry@ccl.net Sun Nov 8 09:45:00 2009 From: "Mahmoud A. A. Ibrahim m.ibrahim1982]|[yahoo.com" To: CCL Subject: CCL: relax the docked complex Message-Id: <-40635-091108091706-16745-n1MHFmEV2EcKQBGe4PDqaA..server.ccl.net> X-Original-From: "Mahmoud A. A. Ibrahim" Content-Type: multipart/alternative; boundary="0-1868677024-1257688213=:93803" Date: Sun, 8 Nov 2009 05:50:13 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim1982:yahoo.com] --0-1868677024-1257688213=:93803 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Jeffrey As I believe, you are going to do Moleculare Mechanics Simulation. Before s= imulation, we usually do minimsation using MM force field inorder to relax/= remove any clashes in the system and then we do equilibration, These two st= eps, as I believe, will treat your system from any errors and your ligand w= ill be fitted, if it should. If you like to do relax your system before these two steps, so you can mini= mise your system (or Only the active site, I would do it if I were you) usi= ng Molecular Mechanics force field or any semi-empirical level using Gaussi= an. I hope it may help you. Sincerely; M. Ibrahim Mahmoud A. A. Ibrahim Current Address School of Chemistry, University of Manchester,=20 Oxford Road, Manchester, M13 9PL, United Kingdom. =20 Home Address =20 Chemistry Department, Faculty of Science,=20 Minia University,=20 Minia 61519,Egypt. Contact Information Email: m.ibrahim*_*compchem.net Email: m.ibrahim1982*_*yahoo.com Website: www.compchem.net Fax No.: +20862342601 =20 --- On Sat, 11/7/09, Yang Mingjun jeffle07^^^163.com wrote: > From: Yang Mingjun jeffle07^^^163.com Subject: CCL: relax the docked complex To: "Ibrahim, Mahmoud A. A. " Date: Saturday, November 7, 2009, 1:25 AM Sent to CCL by: "Yang Mingjun" [jeffle07[a]163.com] Dear all, =A0=A0=A0I am going to perform molecular dynamics simulations of protein-li= gand complex, in=A0 which the ligand is placed into the binding pocket of t= he apo protein by docking methods. A few of the residues in the resulting c= omplex around the ligand should be readjusted to interact properly with the= ligand. However, there is not a guide of how these residues should be adju= sted. I'd like to know how should I fix this problem? Is there any software= or method for the job? Many thanks. Jeffrey -=3D This is automatically added to each message by the mailing script =3D-=A0 =A0 =A0=A0 =A0 =A0Subscribe/Unsubscribe:=20 =A0 =A0 =A0Job: http://www.ccl.net/jobs=20=A0 =A0 =A0=0A=0A=0A --0-1868677024-1257688213=:93803 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable

Dear Jeffrey
As I believe, you are going t= o do Moleculare Mechanics Simulation. Before simulation, we usually do mini= msation using MM force field inorder to relax/remove any clashes in the sys= tem and then we do equilibration, These two steps, as I believe, will treat= your system from any errors and your ligand will be fitted, if it should.<= br>If you like to do relax your system before these two steps, so you can m= inimise your system (or Only the active site, I would do it if I were you) = using Molecular Mechanics force field or any semi-empirical level using Gau= ssian.
I hope it may help you.
Sincerely;
M. Ibrahim

Mahmoud A. A. Ibrahim

Current Address

School of Chemistry= , University of Manchester,
Oxford Road, Manchester, M13 9PL, United Ki= ngdom.

Home Address

= Chemistry Department, Faculty of Science,
Minia Univers= ity,
Minia 61519,Egypt.

Contact Information
Email: m.ibrahim*_*compchem.net
Emai= l: m.ibrahim1982*_*yahoo.com
Website: www.compchem.net
Fax N= o.: +20862342601

--- On Sat, 11/7/09, Y= ang Mingjun jeffle07^^^163.com <owner-chemistry*_*ccl.net> w= rote:

From: Yang Mingjun jeffle07^^^163.com <own= er-chemistry*_*ccl.net>
Subject: CCL: relax the docked complex
To: "= Ibrahim, Mahmoud A. A. " <m.ibrahim1982*_*yahoo.com>
Date: S= aturday, November 7, 2009, 1:25 AM

Sent= to CCL by: "Yang Mingjun" [jeffle07[a]163.com]
Dear all,
= ; I am going to perform molecular dynamics simulations of protein-liga= nd complex, in which the ligand is placed into the binding pocket of = the apo protein by docking methods. A few of the residues in the resulting = complex around the ligand should be readjusted to interact properly with th= e ligand. However, there is not a guide of how these residues should be adj= usted. I'd like to know how should I fix this problem? Is there any softwar= e or method for the job?

Many thanks.

Jeffrey

= -=3D This is automatically added to each message by the mailing script =3D-
To recover the email address of the author of the message, please = change
the strange characters on the top line to the *_* sign. You can als= o
E-mail to= subscribers: CHEMISTRY*_*ccl.net or use:
= ; http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to a= dministrators: CHEMISTRY-REQUEST*_*ccl.net or us= e
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= Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.net/jobs
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=0A=0A=0A=0A --0-1868677024-1257688213=:93803-- From owner-chemistry@ccl.net Sun Nov 8 10:20:01 2009 From: "Mahmoud A. A. Ibrahim m.ibrahim1982:-:yahoo.com" To: CCL Subject: CCL: ONIOM calculations Message-Id: <-40636-091108094158-29150-uA6x8AHIyhTggIoGkQQnkA#%#server.ccl.net> X-Original-From: "Mahmoud A. A. Ibrahim" Content-Type: multipart/alternative; boundary="0-943312989-1257687705=:2649" Date: Sun, 8 Nov 2009 05:41:45 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim1982^_^yahoo.com] --0-943312989-1257687705=:2649 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Roy Let's declear some points here: Is there a difference between treating your system as two QM-B3LYP layers a= nd as one QM-B3LYP layer? in other words, what is the difference between QM= (B3LYP):QM(B3LYP) and=A0 QM(B3LYP) for all the system. As I believe, in gen= eral speaking, they are the same, but in your case, you specify that part A= has a charge of a unit value and part B has a unit value of charge, and du= ring optimization, each part's charge will change with keeping its overall = charge unity. i.e. say, A's charge -1 and B's charge +1, so after optimizat= ion, A's charge will be -1 and B's will be +1, but in case of using only on= e QM(B3LYP) for the whole system, in this case, optimization will lead to a= n overall charge of 0 without any limitation on keeping A's charge equals t= o -1 and B's charge equal to +1. Roy, is it chemically right to make a limitation on the charge of one part = of your system? charge is a big challeng. Take care!!! Roy, I don't know exactly what are you going to do, but have a look on Char= ge Keyword and R.E.D. program, they may open new thinking ways for you. Sincerely; M. Ibrahim Mahmoud A. A. Ibrahim Current Address School of Chemistry, University of Manchester,=20 Oxford Road, Manchester, M13 9PL, United Kingdom. =20 Home Address =20 Chemistry Department, Faculty of Science,=20 Minia University,=20 Minia 61519,Egypt. Contact Information Email: m.ibrahim(!)compchem.net Email: m.ibrahim1982(!)yahoo.com Website: www.compchem.net Fax No.: +20862342601 =20 --- On Sun, 11/8/09, Green Power powergreen^-^gmail.com wrote: > From: Green Power powergreen^-^gmail.com Subject: CCL: ONIOM calculations To: "Ibrahim, Mahmoud A. A. " Date: Sunday, November 8, 2009, 9:15 AM Dear All, Can I have a question about two layer ONIOM calculations. For a A(-)...B(+)= system, I want to learn how the negtive charged A(-) is polarized by the p= ositive charged B(+). I would like to know whether it is meaningfull to use= the same theory levels, say B3LYP, for the two layers. This seems to me li= ke a QM:QM model, instead of QM:MM which seems more meaningfull to me, Your= valuable comments and suggestions are highly appriciated.=20 =0A Roy =0A=0A=0A=0A --0-943312989-1257687705=:2649 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable

Dear Roy
Let's declear some points here:Is there a difference between treating your system as two QM-B3LYP layers= and as one QM-B3LYP layer? in other words, what is the difference between = QM(B3LYP):QM(B3LYP) and QM(B3LYP) for all the system. As I believe, i= n general speaking, they are the same, but in your case, you specify that p= art A has a charge of a unit value and part B has a unit value of charge, a= nd during optimization, each part's charge will change with keeping its ove= rall charge unity. i.e. say, A's charge -1 and B's charge +1, so after opti= mization, A's charge will be -1 and B's will be +1, but in case of using on= ly one QM(B3LYP) for the whole system, in this case, optimization will lead= to an overall charge of 0 without any limitation on keeping A's charge equ= als to -1 and B's charge equal to +1.
Roy, is it chemically right to mak= e a limitation on the charge of one part of your system? charge is a big chall= eng. Take care!!!
Roy, I don't know exactly what are you going to do, bu= t have a look on Charge Keyword and R.E.D. program, they may open new think= ing ways for you.
Sincerely;
M. Ibrahim

Mahmoud A. = A. Ibrahim

Current Address

School of Chemistry, University= of Manchester,
Oxford Road, Manchester, M13 9PL, United Kingdom.

Home Address

Chemistry = Department, Faculty of Science,
Minia University,
M= inia 61519,Egypt.

Contact Informa= tion
Email: m.ibrahim(!)compchem.net
Email: m.ibrahim1982(!)yahoo.= com
Website: www.compchem.net
Fax No.: +20862342601
=

--- On Sun, 11/8/09, Green Power powergreen^-= ^gmail.com <owner-chemistry(!)ccl.net> wrote:

From: Green Power powergreen^-^gmail.com <owner-chemis= try(!)ccl.net>
Subject: CCL: ONIOM calculations
To: "Ibrahim, Mahmou= d A. A. " <m.ibrahim1982(!)yahoo.com>
Date: Sunday, November= 8, 2009, 9:15 AM

Dear All,

Can I h= ave a question about two layer ONIOM calculations. For a A(-)...B(+) system= , I want to learn how the negtive charged A(-) is polarized by the positive charged B(+). I would like to know whether it is meaningfull to u= se the same theory levels, say B3LYP, for the two layers. This seems to me = like a QM:QM model, instead of QM:MM which seems more meaningfull to me, Yo= ur valuable comments and suggestions are highly appriciated.
=0A
Roy=
=0A

=0A=0A=0A=0A --0-943312989-1257687705=:2649-- From owner-chemistry@ccl.net Sun Nov 8 11:33:01 2009 From: "Abhinav Kumar abhinavmarshal]-[gmail.com" To: CCL Subject: CCL:G: Resolution of the Identity approximation Message-Id: <-40637-091108113105-21930-YSPuiWoNMQJZUH0wyZsl5Q|*|server.ccl.net> X-Original-From: "Abhinav Kumar" Date: Sun, 8 Nov 2009 11:31:01 -0500 Sent to CCL by: "Abhinav Kumar" [abhinavmarshal!^!gmail.com] Dear All, I shall be grateful if anyone can taught me how to use Resolution of the Identity approximation for the analysis of the interaction energy between two molecules using G03W. Thanking you in anticipation. With all kind regards. Sincerely Abhinav Kumar Department of Chemistry Lucknow University abhinavmarshal||gmail.com From owner-chemistry@ccl.net Sun Nov 8 12:07:00 2009 From: "Carlos F. Lagos carlos-.-cbuc.cl" To: CCL Subject: CCL:G: relax the docked complex Message-Id: <-40638-091108113706-24339-2EDJULzJLg2FBYOH1oJFpA]|[server.ccl.net> X-Original-From: "Carlos F. Lagos" Content-Type: multipart/alternative; boundary="----=_NextPart_000_000C_01CA6073.B17375C0" Date: Sun, 8 Nov 2009 13:02:14 -0300 MIME-Version: 1.0 Sent to CCL by: "Carlos F. Lagos" [carlos|*|cbuc.cl] This is a multi-part message in MIME format. ------=_NextPart_000_000C_01CA6073.B17375C0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit Hello Jeffrey, it is of most importance if you plan to do MD of protein-ligand complex (es) that the available force-fields on the software you will use be able to parametrizing or have parameters and topologies for the ligand(s). Many MD packages contains force-fields that have parameters for protein, lipids, nucleic acids, metal and classic co-factors, but depending on the ligands you will work, you should be aware of parametrize your ligand before. Cheers QF Carlos F. Lagos Centre for Bioinformatics CBUC, Faculty of Biological Sciences Medicinal Chemistry Laboratory MCL, Faculty of Chemistry P. Universidad Catolica de Chile Portugal 49, Zocalo I 8330025 Santiago-Chile Phone: +56 2 3541911 I http://www.cbuc.cl _____ De: owner-chemistry+carlos==cbuc.cl.:.ccl.net [mailto:owner-chemistry+carlos==cbuc.cl.:.ccl.net] En nombre de Mahmoud A. A. Ibrahim m.ibrahim1982]|[yahoo.com Enviado el: Domingo, 08 de Noviembre de 2009 10:50 Para: Lagos, Carlos F Asunto: CCL: relax the docked complex Dear Jeffrey As I believe, you are going to do Moleculare Mechanics Simulation. Before simulation, we usually do minimsation using MM force field inorder to relax/remove any clashes in the system and then we do equilibration, These two steps, as I believe, will treat your system from any errors and your ligand will be fitted, if it should. If you like to do relax your system before these two steps, so you can minimise your system (or Only the active site, I would do it if I were you) using Molecular Mechanics force field or any semi-empirical level using Gaussian. I hope it may help you. Sincerely; M. Ibrahim Mahmoud A. A. Ibrahim Current Address School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom. Home Address Chemistry Department, Faculty of Science, Minia University, Minia 61519,Egypt. Contact Information Email: m.ibrahim(~)compchem.net Email: m.ibrahim1982(~)yahoo.com Website: www.compchem.net Fax No.: +20862342601 --- On Sat, 11/7/09, Yang Mingjun jeffle07^^^163.com wrote: > From: Yang Mingjun jeffle07^^^163.com Subject: CCL: relax the docked complex To: "Ibrahim, Mahmoud A. A. " Date: Saturday, November 7, 2009, 1:25 AM Sent to CCL by: "Yang Mingjun" [jeffle07[a]163.com] Dear all, I am going to perform molecular dynamics simulations of protein-ligand complex, in which the ligand is placed into the binding pocket of the apo protein by docking methods. A few of the residues in the resulting complex around the ligand should be readjusted to interact properly with the ligand. However, there is not a guide of how these residues should be adjusted. I'd like to know how should I fix this problem? Is there any software or method for the job? Many thanks. Jeffreythe strange characters on the top line to the (~) sign. You can also

Hello Jeffrey, = it is of most importance if you plan to do MD of protein-ligand complex (es) that = the available force-fields on the software you will use be able to parametrizing or = have parameters and topologies for the ligand(s). Many MD packages contains force-fields = that have parameters for protein, lipids, nucleic acids, metal and classic = co-factors, but depending on the ligands you will work, you should be aware of = parametrize your ligand before. Cheers

QF = Carlos F. Lagos
Centre for Bioinformatics CBUC, Faculty of Biological = Sciences

Medicinal = Chemistry Laboratory MCL, Faculty of Chemistry
P. Universidad Catolica de Chile
Portugal 49, Zocalo I 8330025 Santiago-Chile
Phone: +56 2 3541911 I http://www.cbuc.cl

De: owner-chemistry+carlos=3D=3Dcbuc.cl.:.ccl.net [mailto:owner-chemistry+carlos=3D=3Dcbuc.cl.:.ccl.net] En nombre de Mahmoud A. A. Ibrahim = m.ibrahim1982]|[yahoo.com
Enviado el: Domingo, 08 = de Noviembre de 2009 10:50
Para: Lagos, Carlos F =
Asunto: CCL: relax the = docked complex

Dear = Jeffrey
As I believe, you are going to do Moleculare Mechanics Simulation. = Before simulation, we usually do minimsation using MM force field inorder to relax/remove any clashes in the system and then we do equilibration, = These two steps, as I believe, will treat your system from any errors and = your ligand will be fitted, if it should.
If you like to do relax your system before these two steps, so you can minimise your system (or Only the active site, I would do it if I were = you) using Molecular Mechanics force field or any semi-empirical level = using Gaussian.
I hope it may help you.
Sincerely;
M. Ibrahim

Mahmoud A. A. = Ibrahim

Current Address

School of = Chemistry, University of Manchester,
Oxford Road, Manchester, M13 9PL, United = Kingdom.

Home Address

Chemistry = Department, Faculty of Science,
Minia University,
Minia 61519,Egypt.

Contact Information
Email: m.ibrahim(~)compchem.net
Email: m.ibrahim1982(~)yahoo.com
Website: www.compchem.net
Fax No.: +20862342601

--- On Sat, 11/7/09, Yang Mingjun = jeffle07^^^163.com <owner-chemistry(~)ccl.net><= /span> wrote:

From: Yang Mingjun jeffle07^^^163.com = <owner-chemistry(~)ccl.net>
Subject: CCL: relax the docked complex
To: "Ibrahim, Mahmoud A. A. " = <m.ibrahim1982(~)yahoo.com>
Date: Saturday, November 7, 2009, 1:25 AM

Sent to CCL by: "Yang Mingjun" [jeffle07[a]163.com]
Dear all,
I am going to perform molecular dynamics simulations = of protein-ligand complex, in which the ligand is placed into the = binding pocket of the apo protein by docking methods. A few of the residues in = the resulting complex around the ligand should be readjusted to interact = properly with the ligand. However, there is not a guide of how these residues = should be adjusted. I'd like to know how should I fix this problem? Is there = any software or method for the job?

Many thanks.

Jeffrey

-=3D This is automatically added to each message by the mailing script = =3D-
To recover the email address of the author of the message, please = change
the strange characters on the top line to the (~) sign. You can = also<br

E-mail to subscribers: CHEMISTRY(~)ccl.net or = use:
http://www.ccl.net/cgi-bin/ccl/send_ccl_message
=
E-mail to administrators: CHEMISTRY-REQUEST(~)ccl.ne= t or use
http://www.ccl.net/cgi-bin/ccl/send_ccl_message
= <br
http://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

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Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml<= br> <br
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------=_NextPart_000_000C_01CA6073.B17375C0-- From owner-chemistry@ccl.net Sun Nov 8 12:42:01 2009 From: "Morad El-Hendawy m80elhendawy(~)yahoo.com" To: CCL Subject: CCL: ONIOM calculations Message-Id: <-40639-091108115858-2890-jsMWQUARX4KjRfKWsLgCNQ-$-server.ccl.net> X-Original-From: Morad El-Hendawy Content-Type: multipart/alternative; boundary="0-762902846-1257699525=:92354" Date: Sun, 8 Nov 2009 08:58:45 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Morad El-Hendawy [m80elhendawy*|*yahoo.com] --0-762902846-1257699525=:92354 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hey Roy, It is easy to model QM/QM by the same method i.e. B3LYP and the same basis = set e.g. 6-31+G** . You can carry out this using Gaussview. I did a simple = example to check that, CH3+NH- it gave a normal termination and it is right= . Take care, you have to determine the two centeral atoms in both parts, he= re C+ and N-. As you know there is no pure ionic bond, for example the bond= ing between C+ and N- has a partial covalent charecter so you have to set a= suitable distance between two center, here for example 1.5 Ang. Please aft= er you succeed in your calculation, let us know how to overcome difficultie= s faced you. Good luck,=20 ***************************************************************************= ***********************Morad M. El-Hendawy ***************************************************************************= ***********************=A0If you want a happy life, do four things:=A01- Co= ntemplate and be thankful, 2- The past is gone forever, 3- Today all that you have, 4- Leave the future alone until it come.=A0********************************= ***************************************************************************= ******** --- On Sun, 11/8/09, Mahmoud A. A. Ibrahim m.ibrahim1982:-:yahoo.com wrote: > From: Mahmoud A. A. Ibrahim m.ibrahim1982:-:yahoo.com Subject: CCL: ONIOM calculations To: "El-Hendawy, Morad Metwally " Date: Sunday, November 8, 2009, 3:41 PM Dear Roy Let's declear some points here: Is there a difference between treating your system as two QM-B3LYP layers a= nd as one QM-B3LYP layer? in other words, what is the difference between QM= (B3LYP):QM(B3LYP) and=A0 QM(B3LYP) for all the system. As I believe, in gen= eral speaking, they are the same, but in your case, you specify that part A= has a charge of a unit value and part B has a unit value of charge, and du= ring optimization, each part's charge will change with keeping its overall = charge unity. i.e. say, A's charge -1 and B's charge +1, so after optimizat= ion, A's charge will be -1 and B's will be +1, but in case of using only on= e QM(B3LYP) for the whole system, in this case, optimization will lead to a= n overall charge of 0 without any limitation on keeping A's charge equals t= o -1 and B's charge equal to +1. Roy, is it chemically right to make a=0A limitation on the charge of one pa= rt of your system? charge is a big challeng. Take care!!! Roy, I don't know exactly what are you going to do, but have a look on Char= ge Keyword and R.E.D. program, they may open new thinking ways for you. Sincerely; M. Ibrahim Mahmoud A. A. Ibrahim Current Address School of Chemistry, University of Manchester,=20 Oxford Road, Manchester, M13 9PL, United Kingdom. =20 Home Address =20 Chemistry Department,=0A Faculty of Science,=20 Minia University,=20 Minia 61519,Egypt. Contact Information Email: m.ibrahim#,#compchem.net Email: m.ibrahim1982#,#yahoo.com Website: www.compchem.net Fax No.: +20862342601 =20 --- On Sun, 11/8/09, Green Power powergreen^-^gmail.com wrote: > From: Green Power powergreen^-^gmail.com Subject: CCL: ONIOM calculations To: "Ibrahim, Mahmoud A. A. " Date: Sunday, November 8, 2009, 9:15 AM Dear All, Can I have a question about two layer ONIOM calculations. For a A(-)...B(+)= system, I want to learn how the negtive charged A(-) is polarized by the= =0A positive charged B(+). I would like to know whether it is meaningfull t= o use the same theory levels, say B3LYP, for the two layers. This seems to = me like a QM:QM model, instead of QM:MM which seems more meaningfull to me,= Your valuable comments and suggestions are highly appriciated.=20 =0A Roy =0A =0A=0A=0A=0A =0A=0A=0A --0-762902846-1257699525=:92354 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable

Hey Roy,
It is easy to model QM/QM by the = same method i.e. B3LYP and the same basis set e.g. 6-31+G** . You can carry= out this using Gaussview. I did a simple example to check that, CH3+NH- it= gave a normal termination and it is right. Take care, you have to determin= e the two centeral atoms in both parts, here C+ and N-. As you know there i= s no pure ionic bond, for example the bonding between C+ and N- has a parti= al covalent charecter so you have to set a suitable distance between two ce= nter, here for example 1.5 Ang. Please after you succeed in your calculatio= n, let us know how to overcome difficulties faced you.
Good luck,

**************************************************************= ************************************

Morad M. El-Hendawy

******************= ***************************************************************************= *****

= ;If you want = a happy life, do four things:

<= /font>

<= strong>1- Contem= plate and be thankful,
2- The past is gone forever,
3- Today all that you have,
4- Leav= e the future alone until it come.

*******************************************= ************************************************************************

--- On Sun, 11= /8/09, Mahmoud A. A. Ibrahim m.ibrahim1982:-:yahoo.com <owner-chemist= ry]~[ccl.net> wrote:

From: Mahmoud A. A. Ibrahim m.ib= rahim1982:-:yahoo.com <owner-chemistry]~[ccl.net>
Subject: CCL: ONIO= M calculations
To: "El-Hendawy, Morad Metwally " <m80elhendaw= y]~[yahoo.com>
Date: Sunday, November 8, 2009, 3:41 PM

=
Dear Roy
Let's declear some points here:
Is there a = difference between treating your system as two QM-B3LYP layers and as one Q= M-B3LYP layer? in other words, what is the difference between QM(B3LYP):QM(= B3LYP) and QM(B3LYP) for all the system. As I believe, in general spe= aking, they are the same, but in your case, you specify that part A has a c= harge of a unit value and part B has a unit value of charge, and during optimiza= tion, each part's charge will change with keeping its overall charge unity.= i.e. say, A's charge -1 and B's charge +1, so after optimization, A's char= ge will be -1 and B's will be +1, but in case of using only one QM(B3LYP) f= or the whole system, in this case, optimization will lead to an overall cha= rge of 0 without any limitation on keeping A's charge equals to -1 and B's = charge equal to +1.
Roy, is it chemically right to make a=0A limitation = on the charge of one part of your system? charge is a big challeng. Take ca= re!!!
Roy, I don't know exactly what are you going to do, but have a loo= k on Charge Keyword and R.E.D. program, they may open new thinking ways for= you.
Sincerely;
M. Ibrahim
Mahmoud A. A. Ibrahim
Current Address
School of Chemistry, University of Manchester= ,
Oxford Road, Manchester, M13 9PL, United Kingdom.

= Home Address
Chemistry Department,=0A= Faculty of Science,
Minia University,
M= inia 61519,Egypt.

Contact Informa= tion
Email: m.ibrahim#,#compchem.net
Email: m.ibrahim1982#,#ya= hoo.com
Website: www.compchem.net
Fax No.: +20862342601

--- On Sun, 11/8/09, Green Power powergre= en^-^gmail.com <owner-chemistry#,#ccl.net> wrote:

From: Green Power powergreen^-^gmail.com <owner-= chemistry#,#ccl.net>
Subject: CCL: ONIOM calculations
To: "Ibrahim= , Mahmoud A. A. " <m.ibrahim1982#,#yahoo.com>
Date: Sunday, Novemb= er 8, 2009, 9:15 AM

Dear All,

Can I= have a question about two layer ONIOM calculations. For a A(-)...B(+) syst= em, I want to learn how the negtive charged A(-) is polarized by the=0A pos= itive charged B(+). I would like to know whether it is meaningfull to use t= he same theory levels, say B3LYP, for the two layers. This seems to me like= a QM:QM model, instead of QM:MM which seems more meaningfull to me, Your v= aluable comments and suggestions are highly appriciated.
=0A
Roy
= =0A

=0A=0A=0A=0A

=0A=0A --0-762902846-1257699525=:92354-- From owner-chemistry@ccl.net Sun Nov 8 14:21:00 2009 From: "Mahmoud A. A. Ibrahim m.ibrahim1982]=[yahoo.com" To: CCL Subject: CCL: ONIOM calculations Message-Id: <-40640-091108141728-14337-oed03qRzXpEKAJbloTv9fg%%server.ccl.net> X-Original-From: "Mahmoud A. A. Ibrahim" Content-Type: multipart/alternative; boundary="0-225145087-1257707835=:25054" Date: Sun, 8 Nov 2009 11:17:15 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim1982+*+yahoo.com] --0-225145087-1257707835=:25054 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Morad I am so sorry, but I got confused about your reply. i-=A0 I did=0Aa simple example to check that, CH3+NH- it gave a normal term= ination: are you sure about this chemical equation/structure? do you mean: CH3+=A0 += =A0 NH- ,I am really confused ii- Take care, you have to determine the two centeral=0Aatoms in both parts= , here C+ and N- Sorry why should I determine the central atoms and How can I do that? iii- As you know there is no pure ionic=0Abond, for example the bonding bet= ween C+ and N- has a partial covalent=0Acharecter so you have to set a suit= able distance between two center,=0Ahere for example 1.5 Ang. In secondary school, we got that this is a bond called ionic bond, such as = the bond exists between Na+ and Cl- in the salt. But the bond between N and C is a covalent bond, there are polar and non-po= lar covalent bonds. Here, we have polar covalent bond. For Roy, depending on what are you going to do, you should optimize the two= part A and B in presence of each other and then calculate the charge. Sorr= y, it is a big issuse and we don't know what you want to do exactly. Sincerely; M. Ibrahim Mahmoud A. A. Ibrahim Current Address School of Chemistry, University of Manchester,=20 Oxford Road, Manchester, M13 9PL, United Kingdom. =20 Home Address =20 Chemistry Department, Faculty of Science,=20 Minia University,=20 Minia 61519,Egypt. Contact Information Email: m.ibrahim,,compchem.net Email: m.ibrahim1982,,yahoo.com Website: www.compchem.net Fax No.: +20862342601 =20 --- On Sun, 11/8/09, Morad El-Hendawy m80elhendawy(~)yahoo.com wrote: > From: Morad El-Hendawy m80elhendawy(~)yahoo.com Subject: CCL: ONIOM calculations To: "Ibrahim, Mahmoud A. A. " Date: Sunday, November 8, 2009, 4:58 PM Hey Roy, It is easy to model QM/QM by the same method i.e. B3LYP and the same basis = set e.g. 6-31+G** . You can carry out this using Gaussview. I did a simple = example to check that, CH3+NH- it gave a normal termination and it is right= . Take care, you have to determine the two centeral atoms in both parts, he= re C+ and N-. As you know there is no pure ionic bond, for example the bond= ing between C+ and N- has a partial covalent charecter so you have to set a= suitable distance between two center, here for example 1.5 Ang. Please aft= er you succeed in your calculation, let us know how to overcome difficultie= s faced you. Good luck,=20 ***************************************************************************= ***********************Morad M. El-Hendawy ***************************************************************************= ***********************=A0If you want a happy life, do four things:=A01- Co= ntemplate and be thankful, 2- The past is gone forever, 3- Today all that you have, 4- Leave the future alone until it come.=A0********************************= ***************************************************************************= ******** --- On Sun, 11/8/09, Mahmoud A. A. Ibrahim m.ibrahim1982:-:yahoo.com wrote: > From: Mahmoud A. A. Ibrahim m.ibrahim1982:-:yahoo.com Subject: CCL: ONIOM calculations To: "El-Hendawy, Morad Metwally " Date: Sunday, November 8, 2009, 3:41 PM Dear Roy Let's declear some points here: Is there a difference between treating your system as two QM-B3LYP layers a= nd as one QM-B3LYP layer? in other words, what is the difference between QM= (B3LYP):QM(B3LYP) and=A0 QM(B3LYP) for all the system. As I believe, in gen= eral speaking, they are the same, but in your case, you specify that part A= has a charge=0A of a unit value and part B has a unit value of charge, and= during optimization, each part's charge will change with keeping its overa= ll charge unity. i.e. say, A's charge -1 and B's charge +1, so after optimi= zation, A's charge will be -1 and B's will be +1, but in case of using only= one QM(B3LYP) for the whole system, in this case, optimization will lead t= o an overall charge of 0 without any limitation on keeping A's charge equal= s to -1 and B's charge equal to +1. Roy, is it chemically right to make a=0A limitation on the charge of one pa= rt of your system? charge is a big challeng. Take care!!! Roy, I don't know exactly what are you going to do, but have a look on Char= ge Keyword and R.E.D. program, they may open new thinking ways for you. Sincerely; M. Ibrahim Mahmoud A. A. Ibrahim Current Address School of Chemistry, University of Manchester,=20 Oxford Road, Manchester, M13 9PL, United Kingdom. =20 Home Address =20 Chemistry Department,=0A Faculty of Science,=20 Minia University,=20 Minia 61519,Egypt. Contact Information Email: m.ibrahim#,#compchem.net Email: m.ibrahim1982#,#yahoo.com Website: www.compchem.net Fax No.: +20862342601 =20 --- On Sun, 11/8/09, Green Power powergreen^-^gmail.com wrote: > From: Green Power powergreen^-^gmail.com Subject: CCL: ONIOM calculations To: "Ibrahim, Mahmoud A. A. " Date: Sunday, November 8, 2009, 9:15 AM Dear All, Can I have a question about two layer ONIOM calculations. For a A(-)...B(+)= system, I want to learn how the negtive charged A(-) is polarized by the= =0A positive charged B(+). I would like to know whether it is meaningfull t= o use the same theory levels, say B3LYP, for the two layers. This seems to = me like a QM:QM model, instead of QM:MM which seems more meaningfull to me,= Your valuable comments and suggestions are highly appriciated.=20 =0A Roy =0A =0A=0A=0A=0A =20 =0A=0A =0A=0A=0A --0-225145087-1257707835=:25054 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable

Dear Morad
I am so sorry, but I got confus= ed about your reply.
i- I did= =0Aa simple example to check that, CH3+NH- it gave a normal termination:
are you sure about this chemical equation/structure? do you mean: C= H3+ + NH- ,I am really confused
ii- Take care, you have to determine the two centeral=0Aatoms in bo= th parts, here C+ and N-
Sorry why should I determine the central= atoms and How can I do that?
iii- A= s you know there is no pure ionic=0Abond, for example the bonding between C= + and N- has a partial covalent=0Acharecter so you have to set a suitable d= istance between two center,=0Ahere for example 1.5 Ang.
In second= ary school, we got that this is a bond called ionic bond, such as the bond = exists between Na+ and Cl- in the salt.
But the bond between N and C is = a covalent bond, there are polar and non-polar covalent bonds. Here, we hav= e polar covalent bond.

For Roy, depending on what are you going to d= o, you should optimize the two part A and B in presence of each other and t= hen calculate the charge. Sorry, it is a big issuse and we don't know what = you want to do exactly.
Sincerely;
M. Ibrahim

M= ahmoud A. A. Ibrahim

Current Address

School of Chemistry, Un= iversity of Manchester,
Oxford Road, Manchester, M13 9PL, United Kingdom.

Home Ad= dress

Chemistry Department, Faculty of Sci= ence,
Minia University,
Minia 61519,Egyp= t.

Contact Information
= Email: m.ibrahim,,compchem.net
Email: m.ibrahim1982,,yahoo.com
Website:= www.compchem.net
Fax No.: +20862342601

--- On Sun, 11/8/09, Morad El-Hendawy m80elhendawy(~)yahoo.c= om <owner-chemistry,,ccl.net> wrote:

From: Morad El-Hendawy m80elhendawy(~)yahoo.com <owner-chemi= stry,,ccl.net>
Subject: CCL: ONIOM calculations
To: "Ibrahim, Mahmo= ud A. A. " <m.ibrahim1982,,yahoo.com>
Date: Sunday, November 8, = 2009, 4:58 PM

<= /tr>
Hey Roy,
It is easy to model= QM/QM by the same method i.e. B3LYP and the same basis set e.g. 6-31+G** .= You can carry out this using Gaussview. I did a simple example to check th= at, CH3+NH- it gave a normal termination and it is right. Take care, you ha= ve to determine the two centeral atoms in both parts, here C+ and N-. As yo= u know there is no pure ionic bond, for example the bonding between C+ and = N- has a partial covalent charecter so you have to set a suitable distance = between two center, here for example 1.5 Ang. Please after you succeed in y= our calculation, let us know how to overcome difficulties faced you.
Good l= uck,

*********************************************************************= *****************************
Morad M. El-Hendawy

*************************= *************************************************************************
If you want a happy = life, do four things:

<= strong>1- Contem= plate and be thankful,
2- The past is gone forever,
3- Today all that you have,
4- Leav= e the future alone until it come.
*******************************************= ************************************************************************

--- On Sun, 11= /8/09, Mahmoud A. A. Ibrahim m.ibrahim1982:-:yahoo.com <owner-chemist= ry-#-ccl.net> wrote:

From: Mahmoud A. A. Ibrahim m.ib= rahim1982:-:yahoo.com <owner-chemistry-#-ccl.net>
Subject: CCL: ON= IOM calculations
To: "El-Hendawy, Morad Metwally " <m80elhendawy-#-ya= hoo.com>
Date: Sunday, November 8, 2009, 3:41 PM

Dear RoyLet's declear some points here:
Is there a difference between treating = your system as two QM-B3LYP layers and as one QM-B3LYP layer? in other word= s, what is the difference between QM(B3LYP):QM(B3LYP) and QM(B3LYP) f= or all the system. As I believe, in general speaking, they are the same, bu= t in your case, you specify that part A has a charge=0A of a unit value and= part B has a unit value of charge, and during optimization, each part's ch= arge will change with keeping its overall charge unity. i.e. say, A's charg= e -1 and B's charge +1, so after optimization, A's charge will be -1 and B'= s will be +1, but in case of using only one QM(B3LYP) for the whole system,= in this case, optimization will lead to an overall charge of 0 without any= limitation on keeping A's charge equals to -1 and B's charge equal to +1.<= br>Roy, is it chemically right to make a=0A limitation on the charge of one= part of your system? charge is a big challeng. Take care!!!
Roy, I don'= t know exactly what are you going to do, but have a look on Charge Keyword = and R.E.D. program, they may open new thinking ways for you.
Sincerely;<= br>M. Ibrahim
Mahmoud A. A. Ibrahim
C= urrent Address
School of Chemistry, University of Manchester,
Oxford Road, M= anchester, M13 9PL, United Kingdom.

Home Address =
Chemistry Department,=0A Faculty of Science,=
Minia University,
Minia 61519,Egypt.
Contact Information
Email= : m.ibrahim#,#compchem.net
Email: m.ibrahim1982#,#yahoo.com
Website: = www.compchem.net
Fax No.: +20862342601

--- On Sun, 11/8/09, Green Power powergreen^-^gmail.com &l= t;owner-chemistry#,#ccl.net> wrote:
=
From: Green Power powergreen^-^gmail.com <owner-chemistry#,#ccl.net&= gt;
Subject: CCL: ONIOM calculations
To: "Ibrahim, Mahmoud A. A. " &l= t;m.ibrahim1982#,#yahoo.com>
Date: Sunday, November 8, 2009, 9:15 AM<= br>
Dear All,

Can I have a question abo= ut two layer ONIOM calculations. For a A(-)...B(+) system, I want to learn = how the negtive charged A(-) is polarized by the=0A positive charged B(+). = I would like to know whether it is meaningfull to use the same theory level= s, say B3LYP, for the two layers. This seems to me like a QM:QM model, inst= ead of QM:MM which seems more meaningfull to me, Your valuable comments and= suggestions are highly appriciated.
=0A
Roy
=0A

=0A=0A=0A=0A

=0A=0A

=0A=0A --0-225145087-1257707835=:25054-- From owner-chemistry@ccl.net Sun Nov 8 14:55:00 2009 From: "=?ISO-8859-1?Q?Nicolas_Ferr=E9?= nicolas.ferre|a|univ-provence.fr" To: CCL Subject: CCL: ONIOM calculations Message-Id: <-40641-091108135349-11773-lpRQCuaQAG0QhC413CUmYA.:.server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Nicolas_Ferr=E9?= Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Sun, 08 Nov 2009 19:24:08 +0100 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Nicolas_Ferr=E9?= [nicolas.ferre.:.univ-provence.fr] Sorry, but I don't understand the aim of this discussion. The Oniom method is a substractive scheme: E=E(A,high level)-E(A,low level)+E(A+B,low level) In the present case: high level=low level => E=E(A+B)!!! Basically it is a standard non-Oniom calculation. Maybe I miss something, but it seems your calculation is not really meaningfull ... NF Morad El-Hendawy m80elhendawy(~)yahoo.com a �crit : > Hey Roy, > It is easy to model QM/QM by the same method i.e. B3LYP and the same > basis set e.g. 6-31+G** . You can carry out this using Gaussview. I did > a simple example to check that, CH3+NH- it gave a normal termination and > it is right. Take care, you have to determine the two centeral atoms in > both parts, here C+ and N-. As you know there is no pure ionic bond, for > example the bonding between C+ and N- has a partial covalent charecter > so you have to set a suitable distance between two center, here for > example 1.5 Ang. Please after you succeed in your calculation, let us > know how to overcome difficulties faced you. > Good luck, > > **************************************************************************************************** > *Morad M. El-Hendawy* > > **************************************************************************************************** > ** *If you want a happy life, do four things:* > ** > *1- Contemplate and be thankful, > 2- The past is gone forever, > 3- Today all that you have, > 4- Leave the future alone until it come. * > ********************************************************************************************************************* > ** > > --- On *Sun, 11/8/09, Mahmoud A. A. Ibrahim m.ibrahim1982:-:yahoo.com > //* wrote: > > > From: Mahmoud A. A. Ibrahim m.ibrahim1982:-:yahoo.com > > Subject: CCL: ONIOM calculations > To: "El-Hendawy, Morad Metwally " > Date: Sunday, November 8, 2009, 3:41 PM > > Dear Roy > Let's declear some points here: > Is there a difference between treating your system as two QM-B3LYP > layers and as one QM-B3LYP layer? in other words, what is the > difference between QM(B3LYP):QM(B3LYP) and QM(B3LYP) for all the > system. As I believe, in general speaking, they are the same, but in > your case, you specify that part A has a charge of a unit value and > part B has a unit value of charge, and during optimization, each > part's charge will change with keeping its overall charge unity. > i.e. say, A's charge -1 and B's charge +1, so after optimization, > A's charge will be -1 and B's will be +1, but in case of using only > one QM(B3LYP) for the whole system, in this case, optimization will > lead to an overall charge of 0 without any limitation on keeping A's > charge equals to -1 and B's charge equal to +1. > Roy, is it chemically right to make a limitation on the charge of > one part of your system? charge is a big challeng. Take care!!! > Roy, I don't know exactly what are you going to do, but have a look > on Charge Keyword and R.E.D. program, they may open new thinking > ways for you. > Sincerely; > M. Ibrahim > Mahmoud A. A. Ibrahim > Current Address > School of Chemistry, University of Manchester, > Oxford Road, Manchester, M13 9PL, United Kingdom. > > Home Address > Chemistry Department, Faculty of Science, > Minia University, > Minia 61519,Egypt. > > Contact Information > Email: m.ibrahim#,#compchem.net > Email: m.ibrahim1982#,#yahoo.com > Website: www.compchem.net > Fax No.: +20862342601 > > > --- On *Sun, 11/8/09, Green Power powergreen^-^gmail.com > //* wrote: > > > From: Green Power powergreen^-^gmail.com > Subject: CCL: ONIOM calculations > To: "Ibrahim, Mahmoud A. A. " > Date: Sunday, November 8, 2009, 9:15 AM > > Dear All, > > Can I have a question about two layer ONIOM calculations. For a > A(-)...B(+) system, I want to learn how the negtive charged A(-) > is polarized by the positive charged B(+). I would like to know > whether it is meaningfull to use the same theory levels, say > B3LYP, for the two layers. This seems to me like a QM:QM model, > instead of QM:MM which seems more meaningfull to me, Your > valuable comments and suggestions are highly appriciated. > > Roy > > > -- Nicolas Ferre' Laboratoire Chimie Provence Universite' de Provence - France Tel: +33 491282733 http://sites.univ-provence.fr/lcp-ct From owner-chemistry@ccl.net Sun Nov 8 16:12:00 2009 From: "Mahmoud A. A. Ibrahim m.ibrahim1982^-^yahoo.com" To: CCL Subject: CCL:G: Explaination of some parts of Amber output implemented in G03/09 Message-Id: <-40642-091108161039-8920-MxLSiwNFRbfdn+O/mYfVwA]*[server.ccl.net> X-Original-From: "Mahmoud A. A. Ibrahim" Content-Type: multipart/alternative; boundary="0-1457295724-1257714626=:9091" Date: Sun, 8 Nov 2009 13:10:26 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim1982_+_yahoo.com] --0-1457295724-1257714626=:9091 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Morad I am so sorry, I was in a long vacation in home, so I will start to reply o= n your enquiry here on CCL to give a chance to anybody else to read=0Amy re= ply and add any comment: i- the first part is for MM parameters generation: I=3D=A0 =A0 1 IAn=3D=A0 6 Valence=3D36. =A0 =A0 =A0 =A0 =A0 JB=3D=A0 1 J=3D=A0 =A0 2 IAn=3D=A0 6 IBT=3D12 Dist=3D 1= .40D+00 =A0 =A0 =A0 =A0 =A0 JB=3D=A0 2 J=3D=A0 =A0 6 IAn=3D=A0 6 IBT=3D12 Dist=3D 1= .39D+00 =A0 =A0 =A0 =A0 =A0 JB=3D=A0 3 J=3D=A0 =A0 7 IAn=3D=A0 1 IBT=3D 1 Dist=3D 1= .10D+00 here, the first atom in the list (I=3D=A0 =A0 1) having atomic number 6 (IA= n=3D=A0 6), i.e. first Carbon atom, is bonded to three atoms with a one bon= d distance, atom number 2 (which is carbon IAn=3D=A0 6), 6 (which is carbon= IAn=3D=A0 6) and 7 (which is hydrogen IAn=3D=A0 1), with bond length 1.40= D+00, 1.39D+00 and 1.10D+00 respectively. ii- the second part, requested with IOP(4/33=3D3) is the atomic parameters = used Center=A0 VDW =A0 =A0 =A0 1 1.9080 0.0860000 van der waals parameters for atom number 1 (in the list) are 1.9080 and 0.0= 860000 (Radius Well-depth, respectively). NBDir 3 1=A0 =A0 =A0 0=A0 =A0 =A0 0 this is called Non-Bonding direct, means all non-bonding interaction are of= 3 V-type (Arithmetic type) and 1 C-type (Coulomb type of 1/R), and both V-= type and C-type are with no-cutoff (defined with zero and zero, respectivel= y). This describes the complete set of interactions between all pairs of at= om. (see NBPair at the bottom) HrmStr1 1- 2=A0 469.00 1.4000 this is bond paramtere between atom 1 and atom 2 in the list, the bond forc= e constant is 469.00 and equilibrium bond length is 1.4 Ang. HrmBnd1 1- 2- 3=A0 63.00 120.00 this is angle parameter between atom 1, atom 2 and atom 3 in the list, with= 63.00 force constant and 120.0 equilibrium angle. AmbTrs 4- 5- 6- 1=A0=A0=A00 180=A0=A0=A00=A0=A0=A00=A0 0.00 14.50=A0 0.00= =A0 0.00=A0 4.0 this is torsion parameter between atom 4, atom 5, atom 6 and atom 1. ImpTrs11- 6- 5- 4=A0 1.1 180.0 2.0 this one is for imporper torsion parameter. NBPair12-11 3 1=A0 =A0 =A0 0=A0 =A0 =A0 0 -0.500 -0.167 this is called non-bonding term. Here, the non-bonding interation between a= tom 12 and atom 11 with Arithmetic VDW type (defined by 3) scaled by -0.500= without a cut-off and 1/R Coulomb tpye (defined by 1) scaled by -0.167 wit= hout a cut-off. This describes the overcounted pairs (see NBDir). For more information, visit Gaussian website. Sincerely; M. Ibrahim Mahmoud A. A. Ibrahim Current Address School of Chemistry, University of Manchester,=20 Oxford Road, Manchester, M13 9PL, United Kingdom. =20 Home Address =20 Chemistry Department, Faculty of Science,=20 Minia University,=20 Minia 61519,Egypt. Contact Information Email: m.ibrahim-,-compchem.net Email: m.ibrahim1982-,-yahoo.com Website: www.compchem.net Fax No.: +20862342601 =20 --- On Tue, 10/27/09, Morad M El-Hendawy m80elhendawy.:.yahoo.com wrote: > From: Morad M El-Hendawy m80elhendawy.:.yahoo.com Subject: CCL:G: Explaination of some parts of Amber output implemented in G= 03/09 To: "Ibrahim, Mahmoud A. A. " Date: Tuesday, October 27, 2009, 11:13 AM Sent to CCL by: "Morad M El-Hendawy" [m80elhendawy%x%yahoo.com] Dear CLLers, Currently, I am investigated output of Amber implemented in G03. I found so= me parts in it are incomprehensible. This is some parts of output of Benzen= e molecule as a representative example: I=3D=A0 =A0 1 IAn=3D=A0 6 Valence=3D36. =A0 =A0 =A0 =A0 =A0 JB=3D=A0 1 J=3D=A0 =A0 2 IAn=3D=A0 6 IBT=3D12 Dist=3D 1= .40D+00 =A0 =A0 =A0 =A0 =A0 JB=3D=A0 2 J=3D=A0 =A0 6 IAn=3D=A0 6 IBT=3D12 Dist=3D 1= .39D+00 =A0 =A0 =A0 =A0 =A0 JB=3D=A0 3 J=3D=A0 =A0 7 IAn=3D=A0 1 IBT=3D 1 Dist=3D 1= .10D+00 I=3D=A0 =A0 2 IAn=3D=A0 6 Valence=3D36. =A0 =A0 =A0 =A0 =A0 JB=3D=A0 1 J=3D=A0 =A0 3 IAn=3D=A0 6 IBT=3D12 Dist=3D 1= .39D+00 =A0 =A0 =A0 =A0 =A0 JB=3D=A0 2 J=3D=A0 =A0 8 IAn=3D=A0 1 IBT=3D 1 Dist=3D 1= .10D+00 =A0 =A0 =A0 =A0 =A0 JB=3D=A0 3 J=3D=A0 =A0 1 IAn=3D=A0 6 IBT=3D12 Dist=3D 1= .40D+00 I=3D=A0 =A0 3 IAn=3D=A0 6 Valence=3D36. =A0 =A0 =A0 =A0 =A0 JB=3D=A0 1 J=3D=A0 =A0 4 IAn=3D=A0 6 IBT=3D12 Dist=3D 1= .40D+00 =A0 =A0 =A0 =A0 =A0 JB=3D=A0 2 J=3D=A0 =A0 9 IAn=3D=A0 1 IBT=3D 1 Dist=3D 1= .10D+00 =A0 =A0 =A0 =A0 =A0 JB=3D=A0 3 J=3D=A0 =A0 2 IAn=3D=A0 6 IBT=3D12 Dist=3D 1= .39D+00 I=3D=A0 =A0 4 IAn=3D=A0 6 Valence=3D36. =A0 =A0 =A0 =A0 =A0 JB=3D=A0 1 J=3D=A0 =A0 5 IAn=3D=A0 6 IBT=3D12 Dist=3D 1= .39D+00 =A0 =A0 =A0 =A0 =A0 JB=3D=A0 2 J=3D=A0=A0=A010 IAn=3D=A0 1 IBT=3D 1 Dist=3D= 1.10D+00 =A0 =A0 =A0 =A0 =A0 JB=3D=A0 3 J=3D=A0 =A0 3 IAn=3D=A0 6 IBT=3D12 Dist=3D 1= .40D+00 I=3D=A0 =A0 5 IAn=3D=A0 6 Valence=3D36. =A0 =A0 =A0 =A0 =A0 JB=3D=A0 1 J=3D=A0 =A0 6 IAn=3D=A0 6 IBT=3D12 Dist=3D 1= .40D+00 =A0 =A0 =A0 =A0 =A0 JB=3D=A0 2 J=3D=A0=A0=A011 IAn=3D=A0 1 IBT=3D 1 Dist=3D= 1.10D+00 =A0 =A0 =A0 =A0 =A0 JB=3D=A0 3 J=3D=A0 =A0 4 IAn=3D=A0 6 IBT=3D12 Dist=3D 1= .39D+00 Atomic parameters: Center=A0 VDW =A0 =A0 =A0 1 1.9080 0.0860000 =A0 =A0 =A0 2 1.9080 0.0860000 =A0 =A0 =A0 3 1.9080 0.0860000 =A0 =A0 =A0 4 1.9080 0.0860000 =A0 =A0 =A0 5 1.9080 0.0860000 =A0 =A0 =A0 6 1.9080 0.0860000 =A0 =A0 =A0 7 1.4590 0.0150000 =A0 =A0 =A0 8 1.4590 0.0150000 =A0 =A0 =A0 9 1.4590 0.0150000 =A0 =A0=A0=A010 1.4590 0.0150000 =A0 =A0=A0=A011 1.4590 0.0150000 =A0 =A0=A0=A012 1.4590 0.0150000 Molecular mechanics terms: NBDir3 1=A0 =A0 =A0 0=A0 =A0 =A0 0 HrmStr1 1- 2=A0 469.00 1.4000 HrmStr1 1- 6=A0 469.00 1.4000 HrmStr1 1- 7=A0 367.00 1.0800 HrmStr1 2- 3=A0 469.00 1.4000 HrmStr1 2- 8=A0 367.00 1.0800 HrmStr1 3- 4=A0 469.00 1.4000 HrmStr1 3- 9=A0 367.00 1.0800 HrmStr1 4- 5=A0 469.00 1.4000 HrmStr1 4-10=A0 367.00 1.0800 HrmStr1 5- 6=A0 469.00 1.4000 HrmStr1 5-11=A0 367.00 1.0800 HrmStr1 6-12=A0 367.00 1.0800 HrmBnd1 1- 2- 3=A0 63.00 120.00 HrmBnd1 1- 2- 8=A0 35.00 120.00 HrmBnd1 1- 6-12=A0 35.00 120.00 HrmBnd1 1- 6- 5=A0 63.00 120.00 HrmBnd1 2- 3- 4=A0 63.00 120.00 HrmBnd1 2- 3- 9=A0 35.00 120.00 HrmBnd1 2- 1- 6=A0 63.00 120.00 HrmBnd1 2- 1- 7=A0 35.00 120.00 HrmBnd1 3- 4- 5=A0 63.00 120.00 HrmBnd1 3- 4-10=A0 35.00 120.00 HrmBnd1 3- 2- 8=A0 35.00 120.00 HrmBnd1 4- 5- 6=A0 63.00 120.00 HrmBnd1 4- 5-11=A0 35.00 120.00 HrmBnd1 4- 3- 9=A0 35.00 120.00 HrmBnd1 5- 6-12=A0 35.00 120.00 HrmBnd1 5- 4-10=A0 35.00 120.00 HrmBnd1 6- 1- 7=A0 35.00 120.00 HrmBnd1 6- 5-11=A0 35.00 120.00 AmbTrs 6- 1- 2- 3=A0=A0=A00 180=A0=A0=A00=A0=A0=A00=A0 0.00 14.50=A0 0.00= =A0 0.00=A0 4.0 AmbTrs 6- 1- 2- 8=A0=A0=A00 180=A0=A0=A00=A0=A0=A00=A0 0.00 14.50=A0 0.00= =A0 0.00=A0 4.0 AmbTrs 7- 1- 2- 3=A0=A0=A00 180=A0=A0=A00=A0=A0=A00=A0 0.00 14.50=A0 0.00= =A0 0.00=A0 4.0 AmbTrs 7- 1- 2- 8=A0=A0=A00 180=A0=A0=A00=A0=A0=A00=A0 0.00 14.50=A0 0.00= =A0 0.00=A0 4.0 AmbTrs 2- 1- 6-12=A0=A0=A00 180=A0=A0=A00=A0=A0=A00=A0 0.00 14.50=A0 0.00= =A0 0.00=A0 4.0 AmbTrs 2- 1- 6- 5=A0=A0=A00 180=A0=A0=A00=A0=A0=A00=A0 0.00 14.50=A0 0.00= =A0 0.00=A0 4.0 AmbTrs 7- 1- 6-12=A0=A0=A00 180=A0=A0=A00=A0=A0=A00=A0 0.00 14.50=A0 0.00= =A0 0.00=A0 4.0 AmbTrs 7- 1- 6- 5=A0=A0=A00 180=A0=A0=A00=A0=A0=A00=A0 0.00 14.50=A0 0.00= =A0 0.00=A0 4.0 AmbTrs 8- 2- 3- 4=A0=A0=A00 180=A0=A0=A00=A0=A0=A00=A0 0.00 14.50=A0 0.00= =A0 0.00=A0 4.0 AmbTrs 8- 2- 3- 9=A0=A0=A00 180=A0=A0=A00=A0=A0=A00=A0 0.00 14.50=A0 0.00= =A0 0.00=A0 4.0 AmbTrs 1- 2- 3- 4=A0=A0=A00 180=A0=A0=A00=A0=A0=A00=A0 0.00 14.50=A0 0.00= =A0 0.00=A0 4.0 AmbTrs 1- 2- 3- 9=A0=A0=A00 180=A0=A0=A00=A0=A0=A00=A0 0.00 14.50=A0 0.00= =A0 0.00=A0 4.0 AmbTrs 9- 3- 4- 5=A0=A0=A00 180=A0=A0=A00=A0=A0=A00=A0 0.00 14.50=A0 0.00= =A0 0.00=A0 4.0 AmbTrs 9- 3- 4-10=A0=A0=A00 180=A0=A0=A00=A0=A0=A00=A0 0.00 14.50=A0 0.00= =A0 0.00=A0 4.0 AmbTrs 2- 3- 4- 5=A0=A0=A00 180=A0=A0=A00=A0=A0=A00=A0 0.00 14.50=A0 0.00= =A0 0.00=A0 4.0 AmbTrs 2- 3- 4-10=A0=A0=A00 180=A0=A0=A00=A0=A0=A00=A0 0.00 14.50=A0 0.00= =A0 0.00=A0 4.0 AmbTrs10- 4- 5- 6=A0=A0=A00 180=A0=A0=A00=A0=A0=A00=A0 0.00 14.50=A0 0.00= =A0 0.00=A0 4.0 AmbTrs10- 4- 5-11=A0=A0=A00 180=A0=A0=A00=A0=A0=A00=A0 0.00 14.50=A0 0.00= =A0 0.00=A0 4.0 AmbTrs 3- 4- 5- 6=A0=A0=A00 180=A0=A0=A00=A0=A0=A00=A0 0.00 14.50=A0 0.00= =A0 0.00=A0 4.0 AmbTrs 3- 4- 5-11=A0=A0=A00 180=A0=A0=A00=A0=A0=A00=A0 0.00 14.50=A0 0.00= =A0 0.00=A0 4.0 AmbTrs11- 5- 6-12=A0=A0=A00 180=A0=A0=A00=A0=A0=A00=A0 0.00 14.50=A0 0.00= =A0 0.00=A0 4.0 AmbTrs11- 5- 6- 1=A0=A0=A00 180=A0=A0=A00=A0=A0=A00=A0 0.00 14.50=A0 0.00= =A0 0.00=A0 4.0 AmbTrs 4- 5- 6-12=A0=A0=A00 180=A0=A0=A00=A0=A0=A00=A0 0.00 14.50=A0 0.00= =A0 0.00=A0 4.0 AmbTrs 4- 5- 6- 1=A0=A0=A00 180=A0=A0=A00=A0=A0=A00=A0 0.00 14.50=A0 0.00= =A0 0.00=A0 4.0 ImpTrs 2- 6- 1- 7=A0 1.1 180.0 2.0 ImpTrs 8- 3- 2- 1=A0 1.1 180.0 2.0 ImpTrs 9- 4- 3- 2=A0 1.1 180.0 2.0 ImpTrs10- 5- 4- 3=A0 1.1 180.0 2.0 ImpTrs11- 6- 5- 4=A0 1.1 180.0 2.0 ImpTrs12- 1- 6- 5=A0 1.1 180.0 2.0 NBPair 2- 1 3 1=A0 =A0 =A0 0=A0 =A0 =A0 0 -1.000 -1.000 NBPair 3- 1 3 1=A0 =A0 =A0 0=A0 =A0 =A0 0 -1.000 -1.000 NBPair 3- 2 3 1=A0 =A0 =A0 0=A0 =A0 =A0 0 -1.000 -1.000 NBPair 4- 1 3 1=A0 =A0 =A0 0=A0 =A0 =A0 0 -0.500 -0.167 NBPair 4- 2 3 1=A0 =A0 =A0 0=A0 =A0 =A0 0 -1.000 -1.000 NBPair 4- 3 3 1=A0 =A0 =A0 0=A0 =A0 =A0 0 -1.000 -1.000 NBPair 5- 1 3 1=A0 =A0 =A0 0=A0 =A0 =A0 0 -1.000 -1.000 NBPair 5- 2 3 1=A0 =A0 =A0 0=A0 =A0 =A0 0 -0.500 -0.167 NBPair 5- 3 3 1=A0 =A0 =A0 0=A0 =A0 =A0 0 -1.000 -1.000 NBPair 5- 4 3 1=A0 =A0 =A0 0=A0 =A0 =A0 0 -1.000 -1.000 NBPair 6- 1 3 1=A0 =A0 =A0 0=A0 =A0 =A0 0 -1.000 -1.000 NBPair 6- 2 3 1=A0 =A0 =A0 0=A0 =A0 =A0 0 -1.000 -1.000 NBPair 6- 3 3 1=A0 =A0 =A0 0=A0 =A0 =A0 0 -0.500 -0.167 NBPair 6- 4 3 1=A0 =A0 =A0 0=A0 =A0 =A0 0 -1.000 -1.000 NBPair 6- 5 3 1=A0 =A0 =A0 0=A0 =A0 =A0 0 -1.000 -1.000 NBPair 7- 1 3 1=A0 =A0 =A0 0=A0 =A0 =A0 0 -1.000 -1.000 NBPair 7- 2 3 1=A0 =A0 =A0 0=A0 =A0 =A0 0 -1.000 -1.000 NBPair 7- 3 3 1=A0 =A0 =A0 0=A0 =A0 =A0 0 -0.500 -0.167 NBPair 7- 5 3 1=A0 =A0 =A0 0=A0 =A0 =A0 0 -0.500 -0.167 NBPair 7- 6 3 1=A0 =A0 =A0 0=A0 =A0 =A0 0 -1.000 -1.000 NBPair 8- 1 3 1=A0 =A0 =A0 0=A0 =A0 =A0 0 -1.000 -1.000 NBPair 8- 2 3 1=A0 =A0 =A0 0=A0 =A0 =A0 0 -1.000 -1.000 NBPair 8- 3 3 1=A0 =A0 =A0 0=A0 =A0 =A0 0 -1.000 -1.000 NBPair 8- 4 3 1=A0 =A0 =A0 0=A0 =A0 =A0 0 -0.500 -0.167 NBPair 8- 6 3 1=A0 =A0 =A0 0=A0 =A0 =A0 0 -0.500 -0.167 NBPair 8- 7 3 1=A0 =A0 =A0 0=A0 =A0 =A0 0 -0.500 -0.167 NBPair 9- 1 3 1=A0 =A0 =A0 0=A0 =A0 =A0 0 -0.500 -0.167 NBPair 9- 2 3 1=A0 =A0 =A0 0=A0 =A0 =A0 0 -1.000 -1.000 NBPair 9- 3 3 1=A0 =A0 =A0 0=A0 =A0 =A0 0 -1.000 -1.000 NBPair 9- 4 3 1=A0 =A0 =A0 0=A0 =A0 =A0 0 -1.000 -1.000 NBPair 9- 5 3 1=A0 =A0 =A0 0=A0 =A0 =A0 0 -0.500 -0.167 NBPair 9- 8 3 1=A0 =A0 =A0 0=A0 =A0 =A0 0 -0.500 -0.167 NBPair10- 2 3 1=A0 =A0 =A0 0=A0 =A0 =A0 0 -0.500 -0.167 NBPair10- 3 3 1=A0 =A0 =A0 0=A0 =A0 =A0 0 -1.000 -1.000 NBPair10- 4 3 1=A0 =A0 =A0 0=A0 =A0 =A0 0 -1.000 -1.000 NBPair10- 5 3 1=A0 =A0 =A0 0=A0 =A0 =A0 0 -1.000 -1.000 NBPair10- 6 3 1=A0 =A0 =A0 0=A0 =A0 =A0 0 -0.500 -0.167 NBPair10- 9 3 1=A0 =A0 =A0 0=A0 =A0 =A0 0 -0.500 -0.167 NBPair11- 1 3 1=A0 =A0 =A0 0=A0 =A0 =A0 0 -0.500 -0.167 NBPair11- 3 3 1=A0 =A0 =A0 0=A0 =A0 =A0 0 -0.500 -0.167 NBPair11- 4 3 1=A0 =A0 =A0 0=A0 =A0 =A0 0 -1.000 -1.000 NBPair11- 5 3 1=A0 =A0 =A0 0=A0 =A0 =A0 0 -1.000 -1.000 NBPair11- 6 3 1=A0 =A0 =A0 0=A0 =A0 =A0 0 -1.000 -1.000 NBPair11-10 3 1=A0 =A0 =A0 0=A0 =A0 =A0 0 -0.500 -0.167 NBPair12- 1 3 1=A0 =A0 =A0 0=A0 =A0 =A0 0 -1.000 -1.000 NBPair12- 2 3 1=A0 =A0 =A0 0=A0 =A0 =A0 0 -0.500 -0.167 NBPair12- 4 3 1=A0 =A0 =A0 0=A0 =A0 =A0 0 -0.500 -0.167 NBPair12- 5 3 1=A0 =A0 =A0 0=A0 =A0 =A0 0 -1.000 -1.000 NBPair12- 6 3 1=A0 =A0 =A0 0=A0 =A0 =A0 0 -1.000 -1.000 NBPair12- 7 3 1=A0 =A0 =A0 0=A0 =A0 =A0 0 -0.500 -0.167 NBPair12-11 3 1=A0 =A0 =A0 0=A0 =A0 =A0 0 -0.500 -0.167 Actually, I read the G03 manual regarding this part, but it is not enough, = so I would appreciate anyone give me clear answers. All what I need,is the = meaning of every column. Therefore my questions in brief are: 1- I=3D=A0 =A0 1 IAn=3D=A0 6 Valence=3D36. =A0 =A0 =A0 =A0 =A0 JB=3D=A0 1 J=3D=A0 =A0 2 IAn=3D=A0 6 IBT=3D12 Dist=3D 1= .40D+00=20 2-Molecular mechanics terms: NBDir3 1=A0 =A0 =A0 0=A0 =A0 =A0 0 3-AmbTrs 6- 1- 2- 3=A0=A0=A00 180=A0=A0=A00=A0=A0=A00=A0 0.00 14.50=A0 0.00= =A0 0.00=A0 4.0 4-ImpTrs 2- 6- 1- 7=A0 1.1 180.0 2.0 5-NBPair 2- 1 3 1=A0 =A0 =A0 0=A0 =A0 =A0 0 -1.000 -1.000 The detailed answers would be more appreciated. Thanks in advance Morad El-Hendawy Ireland -=3D This is automatically added to each message by the mailing script =3D-=A0 =A0 =A0=A0 =A0 =A0Subscribe/Unsubscribe:=20 =A0 =A0 =A0Job: http://www.ccl.net/jobs=20=A0 =A0 =A0=0A=0A=0A --0-1457295724-1257714626=:9091 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable <= /table>
=0A=0A --0-1457295724-1257714626=:9091-- From owner-chemistry@ccl.net Sun Nov 8 16:46:00 2009 From: "Mahmoud A. A. Ibrahim m.ibrahim1982::yahoo.com" To: CCL Subject: CCL:G: Cutoff, Scaling Factor & Dielectric Constant Message-Id: <-40643-091108161110-9112-rJgIw2zR/3KJ03w7m2ylcQ|-|server.ccl.net> X-Original-From: "Mahmoud A. A. Ibrahim" Content-Type: multipart/alternative; boundary="0-1204593756-1257714658=:63851" Date: Sun, 8 Nov 2009 13:10:58 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim1982**yahoo.com] --0-1204593756-1257714658=:63851 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Morad I am so sorry, I was in a long vacation in home, so I will start to=0Areply= on your enquiry here on CCL to give a chance to anybody else to=0Aread=0Am= y reply and add any comment: Nonbonding interaction in Gaussian can be specified by using the following = keyword: NonBon V-Type C-Type V-Cutoff C-Cutoff VScale1 VScale2 VScale3 CScale1 CSca= le2 CScale3if you are using AMBER force field, as I believe from your preiv= ous emails, so you should define V-type as 3 and C-type as 1. the second an= d third terms for VDW and Coulomb cutoffs respectively. if you are going to= using no cutoff, then define them to zero. The scale factors are defined b= y the latter values. For example: NonBon 3 1 0 0 0.0 0.0 0.5 0.0 0.0 -1.0 =0AThis function specifies the Amber arithmetic van der Waals=0Ainteraction= (defined by 3), 1/R Coulomb interaction(defined by 1), and no cutoffs (def= ined by 0 for VDW and 0 for Coulomb).=20 Van der Waals=0Ainteractions are scaled by 0.0 for atoms one bond distance.= Van der Waals=0Ainteractions are scaled by 0.0 for atoms two bonds distance= .Van der Waals=0Ainteractions are scaled by 0.5 for atoms more than 2 bonds= distance.=20 Coulomb interactions are scaled by 0.0 for atoms one bond distance.=0ACoulo= mb interactions are scaled by 0.0 for atoms two bonds distance.Coulomb inte= ractions are scaled by 1.0/1.2 (defult value defined by -1.0) for atoms mor= e than 2 bonds distance.=20 =0A For more infomation, visit Gaussian website under Moleculare Mechanics page Sincerely; M. Ibrahim Mahmoud A. A. Ibrahim Current Address School of Chemistry, University of Manchester,=20 Oxford Road, Manchester, M13 9PL, United Kingdom. =20 Home Address =20 Chemistry Department, Faculty of Science,=20 Minia University,=20 Minia 61519,Egypt. Contact=0A Information Email: m.ibrahim,+,compchem.net Email: m.ibrahim1982,+,yahoo.com Website: www.compchem.net Fax No.: +20862342601 =20 --- On Sun, 11/1/09, Morad M. El-Hendawy m80elhendawy-$-yahoo.com wrote: > From: Morad M. El-Hendawy m80elhendawy-$-yahoo.com Subject: CCL:G: Cutoff, Scaling Factor & Dielectric Constant To: "Ibrahim, Mahmoud A. A. " Date: Sunday, November 1, 2009, 8:01 PM Sent to CCL by: "Morad M. El-Hendawy" [m80elhendawy#yahoo.com] Dear Colleagues, Could anybody tell me how can specify keywords of cutoff and scaling factor= for non-bonding interactios terms as well as dielectric constant for Amber= calculation in=0A Gaussian 03? Please give me examples and details. Best regards Morad El-Hendawy Ireland -=3D This is automatically added to each message by the mailing script =3D-=A0 =A0 =A0=A0 =A0 =A0Subscribe/Unsubscribe:=20 =A0 =A0 =A0Job: http://www.ccl.net/jobs=20=A0 =A0 =A0=0A=0A=0A --0-1204593756-1257714658=:63851 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable

Dear Morad
I am so sorry, I was in a long = vacation in home, so I will start to reply on your enquiry here on CCL to g= ive a chance to anybody else to read=0Amy reply and add any comment:
i- = the first part is for MM parameters generation:
I=3D 1 IAn= =3D 6 Valence=3D36.
JB=3D = 1 J=3D 2 IAn=3D 6 IBT=3D12 Dist=3D 1.40D+00
&= nbsp; JB=3D 2 J=3D 6 IAn=3D 6= IBT=3D12 Dist=3D 1.39D+00
JB=3D = ; 3 J=3D 7 IAn=3D 1 IBT=3D 1 Dist=3D 1.10D+00

her= e, the first atom in the list (I=3D 1) having atomic number 6 = (IAn=3D 6), i.e. first Carbon atom, is bonded to three atoms with a o= ne bond distance, atom number 2 (= which is carbon IAn=3D 6), 6 (which is carbon IAn=3D 6) and 7= (which is hydrogen IAn=3D 1), with bond length 1.40D+00, 1.3= 9D+00 and 1.10D+00 respectively.

ii- the second part, requested wit= h IOP(4/33=3D3) is the atomic parameters used
Center VDW
1 1.9080 0.0860000=
van der waals parameters for atom number 1 (in the list) are 1.9080 and= 0.0860000 (Radius Well-depth, respectively).

NBDir 3 1 0 0<= br>this is called Non-Bonding direct, means all non-bonding interaction are= of 3 V-type (Arithmetic type) and 1 C-type (Coulomb type of 1/R), and both= V-type and C-type are with no-cutoff (defined with zero and zero, respecti= vely). This describes the complete set of interactions between all pairs of= atom. (see NBPair at the bottom)

HrmBnd1 1- 2- 3 63.00 120.00
this is ang= le parameter between atom 1, atom 2 and atom 3 in the list, with 63.00 forc= e constant and 120.0 equilibrium angle.

AmbTrs 4- 5- 6- 1 &nbs= p; 0 180 0 0 0.00 14.50 = 0.00 0.00 4.0
this is torsion parameter between atom 4, atom= 5, atom 6 and atom 1.

ImpTrs11- 6- 5- 4 1.1 180.0 2.0
thi= s one is for imporper torsion parameter.

NBPair12-11 3 1 &nbs= p; 0 0 -0.500 -0.167
this is called non-bondi= ng term. Here, the non-bonding interation between atom 12 and atom 11 with = Arithmetic VDW type (defined by 3) scaled by -0.500 without a cut-off and 1= /R Coulomb tpye (defined by 1) scaled by -0.167 without a cut-off.
This = describes the overcounted pairs (see NBDir).

For more information, v= isit Gaussian website.
Sincerely;
M. Ibrahim

=

Mahmoud A. A. Ibrahim

Current Address

School = of Chemistry, University of Manchester,
Oxford Road, Manchester, M13 9P= L, United Kingdom.

Home Address <= /span>

Chemistry Department, Faculty of Science,
M= inia University,
Minia 61519,Egypt.

Contact Information
Email: m.ibrahim-,-compchem= .net
Email: m.ibrahim1982-,-yahoo.com
Website: www.compchem.net
Fax No.= : +20862342601

--- On Tue, 10/27/09, Mo= rad M El-Hendawy m80elhendawy.:.yahoo.com <owner-chemistry-,-ccl.net>= ; wrote:

From: Morad M El-Hendawy m= 80elhendawy.:.yahoo.com <owner-chemistry-,-ccl.net>
Subject: CCL:G: = Explaination of some parts of Amber output implemented in G03/09
To: "Ib= rahim, Mahmoud A. A. " <m.ibrahim1982-,-yahoo.com>
Date: Tue= sday, October 27, 2009, 11:13 AM

Sent t= o CCL by: "Morad M El-Hendawy" [m80elhendawy%x%yahoo.com]
Dear CLLers,Currently, I am investigated output of Amber implemented in G03. I found = some parts in it are incomprehensible. This is some parts of output of Benz= ene molecule as a representative example:
I=3D 1 IAn=3D 6 Valence=3D36.
JB=3D&n= bsp; 1 J=3D 2 IAn=3D 6 IBT=3D12 Dist=3D 1.40D+00
&nbs= p; JB=3D 2 J=3D 6 IAn=3D&nbs= p; 6 IBT=3D12 Dist=3D 1.39D+00
JB=3D&= nbsp; 3 J=3D 7 IAn=3D 1 IBT=3D 1 Dist=3D 1.10D+00
I= =3D 2 IAn=3D 6 Valence=3D36.
&nb= sp; JB=3D 1 J=3D 3 IAn=3D 6 IBT=3D12 Dist= =3D 1.39D+00
JB=3D 2 J=3D = 8 IAn=3D 1 IBT=3D 1 Dist=3D 1.10D+00
= JB=3D 3 J=3D 1 IAn=3D 6 IBT=3D12 Dis= t=3D 1.40D+00
I=3D 3 IAn=3D 6 Valence=3D36.
= ; JB=3D 1 J=3D 4 IAn=3D = ; 6 IBT=3D12 Dist=3D 1.40D+00
JB=3D&n= bsp; 2 J=3D 9 IAn=3D 1 IBT=3D 1 Dist=3D 1.10D+00
&nbs= p; JB=3D 3 J=3D 2 IAn=3D 6 IBT=3D12 Di= st=3D 1.39D+00
I=3D 4 IAn=3D 6 Valence=3D36.
&nbs= p; JB=3D 1 J=3D 5 IAn=3D&nbs= p; 6 IBT=3D12 Dist=3D 1.39D+00
JB=3D&= nbsp; 2 J=3D   10 IAn=3D 1 IBT=3D 1 Dist=3D 1.10D+00 JB=3D 3 J=3D 3 IAn= =3D 6 IBT=3D12 Dist=3D 1.40D+00
I=3D 5 IAn=3D = 6 Valence=3D36.
JB=3D 1 J=3D&nb= sp; 6 IAn=3D 6 IBT=3D12 Dist=3D 1.40D+00
&nbs= p; JB=3D 2 J=3D   11 IAn=3D 1 IBT= =3D 1 Dist=3D 1.10D+00
JB=3D 3 = J=3D 4 IAn=3D 6 IBT=3D12 Dist=3D 1.39D+00
Atomic para= meters:
Center VDW
1 1.9080 0.0860000
= 2 1.9080 0.0860000
3 1.9080 0.0860000
4 1.9080 0.0860000
&nbs= p; 5 1.9080 0.0860000
6 1.9080 0.0860000
= 7 1.4590 0.0150000
8 1.4590 0.0150000=
9 1.4590 0.0150000
   10 = 1.4590 0.0150000
   11 1.4590 0.0150000
=    12 1.4590 0.0150000
Molecular mechanics terms:
NB= Dir3 1 0 0
HrmStr1 1- 2 4= 69.00 1.4000
HrmStr1 1- 6 469.00 1.4000
HrmStr1 1- 7 36= 7.00 1.0800
HrmStr1 2- 3 469.00 1.4000
HrmStr1 2- 8 367= .00 1.0800
HrmStr1 3- 4 469.00 1.4000
HrmStr1 3- 9 367.= 00 1.0800
HrmStr1 4- 5 469.00 1.4000
HrmStr1 4-10 367.0= 0 1.0800
HrmStr1 5- 6 469.00 1.4000
HrmStr1 5-11 367.00= 1.0800
HrmStr1 6-12 367.00 1.0800
HrmBnd1 1- 2- 3 63.00 120.00
HrmBnd1 1- 2- 8 35.00 120.00
HrmBnd1 1-= 6-12 35.00 120.00
HrmBnd1 1- 6- 5 63.00 120.00
HrmBnd1= 2- 3- 4 63.00 120.00
HrmBnd1 2- 3- 9 35.00 120.00
HrmB= nd1 2- 1- 6 63.00 120.00
HrmBnd1 2- 1- 7 35.00 120.00
H= rmBnd1 3- 4- 5 63.00 120.00
HrmBnd1 3- 4-10 35.00 120.00 HrmBnd1 3- 2- 8 35.00 120.00
HrmBnd1 4- 5- 6 63.00 120.00=
HrmBnd1 4- 5-11 35.00 120.00
HrmBnd1 4- 3- 9 35.00 120= .00
HrmBnd1 5- 6-12 35.00 120.00
HrmBnd1 5- 4-10 35.00 = 120.00
HrmBnd1 6- 1- 7 35.00 120.00
HrmBnd1 6- 5-11 35.= 00 120.00
AmbTrs 6- 1- 2- 3   0 180   0&n= bsp;  0 0.00 14.50 0.00 0.00 4.0
AmbT= rs 6- 1- 2- 8   0 180   0   0&= nbsp; 0.00 14.50 0.00 0.00 4.0
AmbTrs 7- 1- 2- 3   0 180   0   0 0.00 = 14.50 0.00 0.00 4.0
AmbTrs 7- 1- 2- 8  &nbs= p;0 180   0   0 0.00 14.50 0.00&n= bsp; 0.00 4.0
AmbTrs 2- 1- 6-12   0 180  = ; 0   0 0.00 14.50 0.00 0.00 4.= 0
AmbTrs 2- 1- 6- 5   0 180   0 &nbs= p; 0 0.00 14.50 0.00 0.00 4.0
AmbTrs 7- 1-= 6-12   0 180   0   0 0.= 00 14.50 0.00 0.00 4.0
AmbTrs 7- 1- 6- 5  &= nbsp;0 180   0   0 0.00 14.50 0.0= 0 0.00 4.0
AmbTrs 8- 2- 3- 4   0 180 &n= bsp; 0   0 0.00 14.50 0.00 0.00 = 4.0
AmbTrs 8- 2- 3- 9   0 180   0   0 0.00 14.50 0.00 = ; 0.00 4.0
AmbTrs 1- 2- 3- 4   0 180  &n= bsp;0   0 0.00 14.50 0.00 0.00 4.0 AmbTrs 1- 2- 3- 9   0 180   0  &= nbsp;0 0.00 14.50 0.00 0.00 4.0
AmbTrs 9- 3- 4-= 5   0 180   0   0 0.00 = 14.50 0.00 0.00 4.0
AmbTrs 9- 3- 4-10  &nbs= p;0 180   0   0 0.00 14.50 0.00&n= bsp; 0.00 4.0
AmbTrs 2- 3- 4- 5   0 180  = ; 0   0 0.00 14.50 0.00 0.00 4.= 0
AmbTrs 2- 3- 4-10   0 180   0 &nbs= p; 0 0.00 14.50 0.00 0.00 4.0
AmbTrs10- 4-= 5- 6   0 180   0   0 0.00 14.50 0.00 = ; 0.00 4.0
AmbTrs10- 4- 5-11   0 180  &n= bsp;0   0 0.00 14.50 0.00 0.00 4.0 AmbTrs 3- 4- 5- 6   0 180   0  &= nbsp;0 0.00 14.50 0.00 0.00 4.0
AmbTrs 3- 4- 5-= 11   0 180   0   0 0.00 = 14.50 0.00 0.00 4.0
AmbTrs11- 5- 6-12  &nbs= p;0 180   0   0 0.00 14.50 0.00&n= bsp; 0.00 4.0
AmbTrs11- 5- 6- 1   0 180  = ; 0   0 0.00 14.50 0.00 0.00 4.= 0
AmbTrs 4- 5- 6-12   0 180   0 &nbs= p; 0 0.00 14.50 0.00 0.00 4.0
AmbTrs 4- 5-= 6- 1   0 180   0   0 0.00 14.50 0.00 = ; 0.00 4.0
ImpTrs 2- 6- 1- 7 1.1 180.0 2.0
ImpTrs 8- 3-= 2- 1 1.1 180.0 2.0
ImpTrs 9- 4- 3- 2 1.1 180.0 2.0
Imp= Trs10- 5- 4- 3 1.1 180.0 2.0
ImpTrs11- 6- 5- 4 1.1 180.0 2.= 0
ImpTrs12- 1- 6- 5 1.1 180.0 2.0
NBPair 2- 1 3 1 = ; 0 0 -1.000 -1.000
NBPair 3- 1 3 1 &n= bsp; 0 0 -1.000 -1.000
NBPair 3- 2 3 1 = 0 0 -1.000 -1.000
NBPair 4- 1 3 1&nb= sp; 0 0 -0.500 -0.167
NBPair 4- 2 3 1= 0 0 -1.000 -1.000
NBPair 4- 3 = 3 1 0 0 -1.000 -1.000
NBPair 5-= 1 3 1 0 0 -1.000 -1.000
NBPair= 5- 2 3 1 0 0 -0.500 -0.167
NBPair 5- 3 3 1 0 0 -1.= 000 -1.000
NBPair 5- 4 3 1 0 0 = -1.000 -1.000
NBPair 6- 1 3 1 0 = 0 -1.000 -1.000
NBPair 6- 2 3 1 0 &nb= sp; 0 -1.000 -1.000
NBPair 6- 3 3 1 0 = 0 -0.500 -0.167
NBPair 6- 4 3 1 0 &nbs= p; 0 -1.000 -1.000
NBPair 6- 5 3 1 0 &= nbsp; 0 -1.000 -1.000
NBPair 7- 1 3 1 0 = ; 0 -1.000 -1.000
NBPair 7- 2 3 1 0&n= bsp; 0 -1.000 -1.000
NBPair 7- 3 3 1 = 0 0 -0.500 -0.167
NBPair 7- 5 3 1 &nbs= p; 0 0 -0.500 -0.167
NBPair 7- 6 3 1 &= nbsp; 0 0 -1.000 -1.000
NBPair 8- 1 3 1 0 0 -1.000 -1.000
NBPair 8- = 2 3 1 0 0 -1.000 -1.000
NBPair = 8- 3 3 1 0 0 -1.000 -1.000
NBPa= ir 8- 4 3 1 0 0 -0.500 -0.167
N= BPair 8- 6 3 1 0 0 -0.500 -0.167 NBPair 8- 7 3 1 0 0 -0.500 -0.167=
NBPair 9- 1 3 1 0 0 -0.500 -0.= 167
NBPair 9- 2 3 1 0 0 -1.000 = -1.000
NBPair 9- 3 3 1 0 0 -1.0= 00 -1.000
NBPair 9- 4 3 1 0 0 -= 1.000 -1.000
NBPair 9- 5 3 1 0 = 0 -0.500 -0.167
NBPair 9- 8 3 1 0 &nbs= p; 0 -0.500 -0.167
NBPair10- 2 3 1 0 0 -0.500 -0.167
NBPair10- 3 3 1 0&nb= sp; 0 -1.000 -1.000
NBPair10- 4 3 1 0= 0 -1.000 -1.000
NBPair10- 5 3 1 = ; 0 0 -1.000 -1.000
NBPair10- 6 3 1 &n= bsp; 0 0 -0.500 -0.167
NBPair10- 9 3 1 = 0 0 -0.500 -0.167
NBPair11- 1 3 1 &nb= sp; 0 0 -0.500 -0.167
NBPair11- 3 3 1 = 0 0 -0.500 -0.167
NBPair11- 4 3 1&nbs= p; 0 0 -1.000 -1.000
NBPair11- 5 3 1&= nbsp; 0 0 -1.000 -1.000
NBPair11- 6 3= 1 0 0 -1.000 -1.000
NBPair11-1= 0 3 1 0 0 -0.500 -0.167
NBPair1= 2- 1 3 1 0 0 -1.000 -1.000
NBPair12- 2 3 1 0 0 -0.= 500 -0.167
NBPair12- 4 3 1 0 0 = -0.500 -0.167
NBPair12- 5 3 1 0 = 0 -1.000 -1.000
NBPair12- 6 3 1 0 &nb= sp; 0 -1.000 -1.000
NBPair12- 7 3 1 0 = 0 -0.500 -0.167
NBPair12-11 3 1 0 &nbs= p; 0 -0.500 -0.167

Actually, I read the G03 manual regarding = this part, but it is not enough, so I would appreciate anyone give me clear= answers. All what I need,is the meaning of every column. Therefore my ques= tions in brief are:

1- I=3D 1 IAn=3D 6 Valence=3D= 36.
JB=3D 1 J=3D 2= IAn=3D 6 IBT=3D12 Dist=3D 1.40D+00
2-Molecular mechanics terms:<= br> NBDir3 1 0 0
3-AmbTrs 6- 1- = 2- 3   0 180   0   0 0.00 = 14.50 0.00 0.00 4.0
4-ImpTrs 2- 6- 1- 7 1.1 180.= 0 2.0
5-NBPair 2- 1 3 1 0 0 -1.0= 00 -1.000

The detailed answers would be more appreciated.
Thanks = in advance
Morad El-Hendawy
Ireland

-=3D This is autom= atically added to each message by the mailing script =3D-
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NonBon V-Type C-Type = V-Cutoff C-Cutoff VScale1 VScale2 VScale3 CScale1 CScale2 CScale3

if you are using AMBER force field, as I believe from your preivous em= ails, so you should define V-type as 3 and C-type as 1. the second and thir= d terms for VDW and Coulomb cutoffs respectively. if you are going to using= no cutoff, then define them to zero. The scale factors are defined by the = latter values.

For example:

NonBon 3 1 0 0 0.0 0.0 0.5 0.0 0.0 -1.0
=0A
This functio= n specifies the Amber arithmetic van der Waals=0Ainteraction (defined by 3), 1/R Coulomb interaction(defined= by 1), and no cutoffs (defined b= y 0 for VDW and 0 for Coulomb).
Van der Waals=0Ainterac= tions are scaled by 0.0 for atoms= one bond distance.
Van der Waals=0Ainteractions are scaled by 0.0 for atoms two bonds distance.
Van der Waals=0Ainteractions are scaled by 0.5 for atoms more than 2 bonds distance.
Coulomb int= eractions are scaled by 0.0 for a= toms one bond distance.=0A
Coulomb interactions are scaled by 0.0 for atoms two bonds distance.
= Coulomb interactions are scaled by 1.0/1.2 (defult value defined by -1.0)= for atoms more than 2 bonds distance.
=0A

For more infom= ation, visit Gaussian website under Moleculare Mechanics page
Sincerely;=
M. Ibrahim

Mahmoud A. A. Ibrahim
Current Address
School of Chemistry, University of Manchester,
Oxford Ro= ad, Manchester, M13 9PL, United Kingdom.

Home Addre= ss
Chemistry Department, Faculty of Scienc= e,
Minia University,
Minia 61519,Egypt.<= br>
Contact=0A Information
= Email: m.ibrahim,+,compchem.net
Email: m.ibrahim1982,+,yahoo.com
Website:= www.compchem.net
Fax No.: +20862342601

--- On Sun, 11/1/09, Morad M. El-Hendawy m80elhendawy-$-yaho= o.com <owner-chemistry,+,ccl.net> wrote:

From: Morad M. El-Hendawy m80elhendawy-$-yahoo.com <owner-c= hemistry,+,ccl.net>
Subject: CCL:G: Cutoff, Scaling Factor & Dielec= tric Constant
To: "Ibrahim, Mahmoud A. A. " <m.ibrahim1982,+,ya= hoo.com>
Date: Sunday, November 1, 2009, 8:01 PM

Sent to CCL by: "Morad M. El-Hendawy" [m80elhendawy#yahoo.c= om]
Dear Colleagues,
Could anybody tell me how can specify keywords o= f cutoff and scaling factor for non-bonding interactios terms as well as di= electric constant for Amber calculation in=0A Gaussian 03? Please give me e= xamples and details.
Best regards
Morad El-Hendawy
Ireland

=

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=0A=0A=0A=0A --0-1204593756-1257714658=:63851-- From owner-chemistry@ccl.net Sun Nov 8 17:24:01 2009 From: "Morad El-Hendawy m80elhendawy]|[yahoo.com" To: CCL Subject: CCL: ONIOM calculations Message-Id: <-40644-091108160954-8741-Ly2wGsETIRVEQ65vxdGksw.:.server.ccl.net> X-Original-From: Morad El-Hendawy Content-Type: multipart/alternative; boundary="0-404032440-1257710980=:18198" Date: Sun, 8 Nov 2009 12:09:40 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Morad El-Hendawy [m80elhendawy,yahoo.com] --0-404032440-1257710980=:18198 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Mahmoud, Thanks for your reply. I would like to explain the following: 1- There is no pure ionic bond, why? Because actually there is no complete = electron transfer between two atoms. In contrast, there is pure covalent bo= nd e.g. H2 because in this case there is equal sharing. To confirm this ple= ase see this information from this fundemental book [Chemical bonds: An int= roduction to atomic and molecular structure, Harry B.Gray] (page 53): http:= //books.google.ie/books?id=3DJj3GAfcRFmsC&pg=3DPA53&lpg=3DPA53&dq=3Dwhy+the= re+is+no+pure+ionic+bond&source=3Dbl&ots=3DIpDp9nLPvt&sig=3DReI4QkjRwoMxW-F= IDoShUyBxjP0&hl=3Den&ei=3DpBv3SoPCI8mH4QbS3_XgAw&sa=3DX&oi=3Dbook_result&ct= =3Dresult&resnum=3D1&ved=3D0CAgQ6AEwAA#v=3Donepage&q=3Dwhy%20there%20is%20n= o%20pure%20ionic%20bond&f=3Dtrue 2- Secondly, Roy mentioned that his system is A+B-, this model can be examp= lified by inorganic complex or organic molecule (stable intermediate or eve= n reactant) e.g. (CH3)4N+H3PO4-. I know that CH3+NH- may not be correct but= it just for simplification. because such molecule may appear as intermedia= te. Just this is succeeded you can apply the same idea on larger systems. 3- Thirdly, you have to specify both centers and adjust the distance betwee= n them. This is normal because both centeres are attracted to each other. A= nd the bond between them have some covalent character so you can express th= is by suitable distance. 4- For your statement "But the bond between N and C is a covalent bond, the= re are polar and=0Anon-polar covalent bonds. Here, we have polar covalent b= ond" this what I expressed in my last message. In some books, some people c= onsider the ionic bond is a very strong polar bond according to Fajan's ru= le. By the way, in this example both parts are optimized in presence of each ot= her. I am happy by such discussion, so please accept my best regards =A0 ***************************************************************************= ***********************Morad M. El-Hendawy*********************************= *****************************************************************=A0If you = want a happy life, do four things:=A01- Contemplate and be thankful, 2- The past is gone forever, 3- Today all that you have, 4- Leave the future alone until it come.=A0********************************= ***************************************************************************= ******** --- On Sun, 11/8/09, Mahmoud A. A. Ibrahim m.ibrahim1982]=3D[yahoo.com wrote: > From: Mahmoud A. A. Ibrahim m.ibrahim1982]=3D[yahoo.com Subject: CCL: ONIOM calculations To: "El-Hendawy, Morad Metwally " Date: Sunday, November 8, 2009, 9:17 PM Dear Morad I am so sorry, but I got confused about your reply. i-=A0 I did=0Aa simple example to check that, CH3+NH- it gave a normal term= ination: are you sure about this chemical equation/structure? do you mean: CH3+=A0 += =A0 NH- ,I am really confused ii- Take care, you have to determine the two centeral=0Aatoms in both parts= , here C+ and N- Sorry why should I determine the central atoms and How can I do that? iii- As you know there is no pure ionic=0Abond, for example the bonding bet= ween C+ and N- has a partial covalent=0Acharecter so you have to set a suit= able distance between two center,=0Ahere for example 1.5 Ang. In secondary school, we got that this is a bond called ionic bond, such as = the bond exists between Na+ and Cl- in the salt. But the bond between N and C is a covalent bond, there are polar and non-po= lar covalent bonds. Here, we have polar covalent bond. For Roy, depending on what are you going to do, you should optimize the two= part A and B in presence of each other and then calculate the charge. Sorr= y, it is a big issuse and we don't know what you want to do exactly. Sincerely; M. Ibrahim Mahmoud A. A. Ibrahim Current Address School of Chemistry, University of Manchester,=20 Oxford=0A Road, Manchester, M13 9PL, United Kingdom. =20 Home Address =20 Chemistry Department, Faculty of Science,=20 Minia University,=20 Minia 61519,Egypt. Contact Information Email: m.ibrahim- -compchem.net Email: m.ibrahim1982- -yahoo.com Website: www.compchem.net Fax No.: +20862342601 =20 --- On Sun, 11/8/09, Morad El-Hendawy m80elhendawy(~)yahoo.com wrote: > From: Morad El-Hendawy m80elhendawy(~)yahoo.com Subject: CCL: ONIOM calculations To: "Ibrahim, Mahmoud A.=0A A. " Date: Sunday, November 8, 2009, 4:58 PM Hey Roy, It is easy to model QM/QM by the same method i.e. B3LYP and the same basis = set e.g. 6-31+G** . You can carry out this using Gaussview. I did a simple = example to check that, CH3+NH- it gave a normal termination and it is right= . Take care, you have to determine the two centeral atoms in both parts, he= re C+ and N-. As you know there is no pure ionic bond, for example the bond= ing between C+ and N- has a partial covalent charecter so you have to set a= suitable distance between two center, here for example 1.5 Ang. Please aft= er you succeed in your=0A calculation, let us know how to overcome difficul= ties faced you. Good luck,=20 ***************************************************************************= ***********************Morad M. El-Hendawy ***************************************************************************= ***********************=A0If you want a happy life, do four things:=A01- Co= ntemplate and be thankful, 2- The past is gone forever, 3- Today all that you have, 4- Leave the future alone until it come.=A0********************************= ***************************************************************************= ******** --- On Sun, 11/8/09, Mahmoud A. A. Ibrahim m.ibrahim1982:-:yahoo.com wrote: > From: Mahmoud A. A. Ibrahim m.ibrahim1982:-:yahoo.com Subject: CCL: ONIOM calculations To: "El-Hendawy, Morad Metwally " Date: Sunday, November 8, 2009, 3:41 PM Dear Roy Let's declear some points here: Is there a difference between treating your system as two QM-B3LYP layers a= nd as one QM-B3LYP layer? in other words, what is the difference between QM= (B3LYP):QM(B3LYP) and=A0 QM(B3LYP) for all the system. As I believe, in gen= eral speaking, they are the same, but in your case, you specify that part A= has a charge=0A of a unit value and part B has a unit value of charge, and= during optimization, each part's charge will change with keeping its overa= ll charge unity. i.e. say, A's charge -1 and B's charge +1, so after optimi= zation, A's charge will be -1 and B's will be +1, but in case of using only= one QM(B3LYP) for the whole system, in this case, optimization will lead t= o an overall charge of 0 without any limitation on keeping A's charge equal= s to -1 and B's charge equal to +1. Roy, is it chemically right to make a=0A limitation on the charge of one pa= rt of your system? charge is a big challeng. Take care!!! Roy, I don't know exactly what are you going to do, but have a look on Char= ge Keyword and R.E.D. program, they may open new thinking ways for you. Sincerely; M. Ibrahim Mahmoud A. A. Ibrahim Current Address School of Chemistry, University of Manchester,=20 Oxford Road, Manchester, M13 9PL, United Kingdom. =20 Home Address =20 Chemistry Department,=0A Faculty of Science,=20 Minia University,=20 Minia 61519,Egypt. Contact Information Email: m.ibrahim#,#compchem.net Email: m.ibrahim1982#,#yahoo.com Website: www.compchem.net Fax No.: +20862342601 =20 --- On Sun, 11/8/09, Green Power powergreen^-^gmail.com wrote: > From: Green Power powergreen^-^gmail.com Subject: CCL: ONIOM calculations To: "Ibrahim, Mahmoud A. A. " Date: Sunday, November 8, 2009, 9:15 AM Dear All, Can I have a question about two layer ONIOM calculations. For a A(-)...B(+)= system, I want to learn how the negtive charged A(-) is polarized by the= =0A positive charged B(+). I would like to know whether it is meaningfull t= o use the same theory levels, say B3LYP, for the two layers. This seems to = me like a QM:QM model, instead of QM:MM which seems more meaningfull to me,= Your valuable comments and suggestions are highly appriciated.=20 =0A Roy =0A =0A=0A=0A=0A =20 =0A=0A =20 =0A=0A =0A=0A=0A --0-404032440-1257710980=:18198 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable

Dear Mahmoud,
Thanks for your reply. I wou= ld like to explain the following:
1- There is no pure ionic bond, why? B= ecause actually there is no complete electron transfer between two atoms. I= n contrast, there is pure covalent bond e.g. H2 because in this case there = is equal sharing. To confirm this please see this information from this fun= demental book [Chemical bonds: An introduction to atomic and molecular stru= cture, Harry B.Gray] (page 53): http://books.google.ie/books?id=3DJj3GAfcRF= msC&pg=3DPA53&lpg=3DPA53&dq=3Dwhy+there+is+no+pure+ionic+bond&a= mp;source=3Dbl&ots=3DIpDp9nLPvt&sig=3DReI4QkjRwoMxW-FIDoShUyBxjP0&a= mp;hl=3Den&ei=3DpBv3SoPCI8mH4QbS3_XgAw&sa=3DX&oi=3Dbook_result&= amp;ct=3Dresult&resnum=3D1&ved=3D0CAgQ6AEwAA#v=3Donepage&q=3Dwh= y%20there%20is%20no%20pure%20ionic%20bond&f=3Dtrue

2- Secondly, = Roy mentioned that his system is A+B-, this model can be examplified by inorganic complex or organic molecu= le (stable intermediate or even reactant) e.g. (CH3)4N+H3PO4-. I know that = CH3+NH- may not be correct but it just for simplification. because such mol= ecule may appear as intermediate. Just this is succeeded you can apply the = same idea on larger systems.

3- Thirdly, you have to specify both ce= nters and adjust the distance between them. This is normal because both cen= teres are attracted to each other. And the bond between them have some cova= lent character so you can express this by suitable distance.

4- For = your statement "But the bond between N and C is a covalent bond, there are = polar and=0Anon-polar covalent bonds. Here, we have polar covalent bond" th= is what I expressed in my last message. In some books, some people consider= the ionic bond is a very strong polar bond according to Fajan's rule.
=
By the way, in this example both parts are optimized in presence of eac= h other.
I am happy by such discussion, so please accept my best regards=

*= ***************************************************************************= **********************

Morad M. El-Hendawy

***************************************************************= ***********************************

<= /strong> If you want a happy life, do four things:<= /div>

1- Contemplate and be thankful,
= 2- The past is gone f= orever,
3- Today all that you have,
4- Leave the future alone until it come. <= /font>
**********************= ***************************************************************************= ******************

=
--- On Sun, 11/8/09, Mahmoud A. A. Ibrahim m.ibrahim1982]=3D[yahoo.c= om <owner-chemistry-,-ccl.net> wrote:

From: Mahmoud A. A. Ibrahim m.ibrahim1982]=3D[yahoo.com <own= er-chemistry-,-ccl.net>
Subject: CCL: ONIOM calculations
To: "El-Hen= dawy, Morad Metwally " <m80elhendawy-,-yahoo.com>
Date: Sund= ay, November 8, 2009, 9:17 PM

Dear Morad
I am so sorry,= but I got confused about your reply.
i- I did=0Aa simple example to check that, CH3+NH- it gave a normal= termination:
are you sure about this chemical equation/structure= ? do you mean: CH3+ + NH- ,I am really confused
ii- Take care, you have to determine the two center= al=0Aatoms in both parts, here C+ and N-
Sorry why should I deter= mine the central atoms and How can I do that?
iii- As you know there is no pure ionic=0Abond, for example the b= onding between C+ and N- has a partial covalent=0Acharecter so you have to = set a suitable distance between two center,=0Ahere for example 1.5 Ang.
In secondary school, we got that this is a bond called ionic bond, s= uch as the bond exists between Na+ and Cl- in the salt.
But the bond bet= ween N and C is a covalent bond, there are polar and non-polar covalent bon= ds. Here, we have polar covalent bond.

For Roy, depending on what ar= e you going to do, you should optimize the two part A and B in presence of = each other and then calculate the charge. Sorry, it is a big issuse and we = don't know what you want to do exactly.
Sincerely;
M. Ibrahim

=
Mahmoud A. A. Ibrahim
Current Address
School = of Chemistry, University of Manchester,
Oxford=0A Road, Manchester, M13= 9PL, United Kingdom.

Home Address =
Chemistry Department, Faculty of Science,
= Minia University,
Minia 61519,Egypt.

Contact Information
Email: m.ibrahim- -com= pchem.net
Email: m.ibrahim1982- -yahoo.com
Website: www.compchem.net<= br> Fax No.: +20862342601

--- On= Sun, 11/8/09, Morad El-Hendawy m80elhendawy(~)yahoo.com <owner-ch= emistry- -ccl.net> wrote:

From: = Morad El-Hendawy m80elhendawy(~)yahoo.com <owner-chemistry- -ccl.net>=
Subject: CCL: ONIOM calculations
To: "Ibrahim, Mahmoud A.=0A A. " <m.ibrahim1982- -yahoo.com>
Date: Sunday, Nove= mber 8, 2009, 4:58 PM

Hey Roy,
It is easy to model QM/QM by the = same method i.e. B3LYP and the same basis set e.g. 6-31+G** . You can carry= out this using Gaussview. I did a simple example to check that, CH3+NH- it= gave a normal termination and it is right. Take care, you have to determin= e the two centeral atoms in both parts, here C+ and N-. As you know there i= s no pure ionic bond, for example the bonding between C+ and N- has a parti= al covalent charecter so you have to set a suitable distance between two ce= nter, here for example 1.5 Ang. Please after you succeed in your=0A calcula= tion, let us know how to overcome difficulties faced you.
Good luck,
**= ***************************************************************************= *********************
Morad M. El-Hendawy
********************************= ******************************************************************
If you want a happy life, d= o four things:

1- Contemplate and be thankful,
2- The past is gone forever,
3-= Today all that you have,
4- Leave the future alone until it come.
*******= ***************************************************************************= *********************************

--- On Sun, 11/8/09, Mahmoud A. A. Ibrahim m.ibrahim1= 982:-:yahoo.com <owner-chemistry-#-ccl.net> wrote:

From: Mahmoud A. A. Ibrahim m.ibrahim1982:-:yahoo.com <= ;owner-chemistry-#-ccl.net>
Subject: CCL: ONIOM calculations
To: "= El-Hendawy, Morad Metwally " <m80elhendawy-#-yahoo.com>
Date: Sund= ay, November 8, 2009, 3:41 PM

Dear Roy
Let's declear some point= s here:
Is there a difference between treating your system as two QM-B3L= YP layers and as one QM-B3LYP layer? in other words, what is the difference= between QM(B3LYP):QM(B3LYP) and QM(B3LYP) for all the system. As I b= elieve, in general speaking, they are the same, but in your case, you speci= fy that part A has a charge=0A of a unit value and part B has a unit value of char= ge, and during optimization, each part's charge will change with keeping it= s overall charge unity. i.e. say, A's charge -1 and B's charge +1, so after= optimization, A's charge will be -1 and B's will be +1, but in case of usi= ng only one QM(B3LYP) for the whole system, in this case, optimization will= lead to an overall charge of 0 without any limitation on keeping A's charg= e equals to -1 and B's charge equal to +1.
Roy, is it chemically right t= o make a=0A limitation on the charge of one part of your system? charge is = a big challeng. Take care!!!
Roy, I don't know exactly what are you goin= g to do, but have a look on Charge Keyword and R.E.D. program, they may ope= n new thinking ways for you.
Sincerely;
M. Ibrahim
= Mahmoud A. A. Ibrahim
<= span style=3D"font-weight: bold;">
Current Address
<= div style=3D"margin-left: 40px; text-align: center;">School of Chemistry, U= niversity of Manchester,
Oxford Road, Manchester, M13 9PL, United Kingd= om.

Home Address
C= hemistry Department,=0A Faculty of Science,
Minia Univers= ity,
Minia 61519,Egypt.

Contact Information
Email: m.ibrahim#,#compchem.net
Em= ail: m.ibrahim1982#,#yahoo.com
Website: www.compchem.net
F= ax No.: +20862342601

--- On Sun, 11/8/0= 9, Green Power powergreen^-^gmail.com <owner-chemistry#,#ccl.net><= /i> wrote:

From: Green Power powergreen= ^-^gmail.com <owner-chemistry#,#ccl.net>
Subject: CCL: ONIOM calcu= lations
To: "Ibrahim, Mahmoud A. A. " <m.ibrahim1982#,#yahoo.com><= br>Date: Sunday, November 8, 2009, 9:15 AM

Dear All,

Can I have a question about two layer ONIOM calculations.= For a A(-)...B(+) system, I want to learn how the negtive charged A(-) is = polarized by the=0A positive charged B(+). I would like to know whether it = is meaningfull to use the same theory levels, say B3LYP, for the two layers= . This seems to me like a QM:QM model, instead of QM:MM which seems more me= aningfull to me, Your valuable comments and suggestions are highly appricia= ted.
=0A
Roy
=0A

= =0A=0A=0A=0A

=0A=0A =

=0A=0A

=0A=0A --0-404032440-1257710980=:18198-- From owner-chemistry@ccl.net Sun Nov 8 17:57:00 2009 From: "Green Power powergreen*_*gmail.com" To: CCL Subject: CCL: ONIOM calculations Message-Id: <-40645-091108162800-16412-y/n2EmdaxcXiz6XZcvIzow_._server.ccl.net> X-Original-From: Green Power Content-Type: multipart/alternative; boundary=00c09fa217a7f1e40a0477e2a198 Date: Sun, 8 Nov 2009 16:19:30 -0500 MIME-Version: 1.0 Sent to CCL by: Green Power [powergreen{}gmail.com] --00c09fa217a7f1e40a0477e2a198 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Mahmoud, Morad and Nicolas, First, thank you for your comments. Maybe I should describe more question more clearly. In a VB model, a diatomic bond can be simply described by spi= n paring, A-B, A(-)-B(+) and A(+)-B(-1). In VB picture, we can easily learn the relative weight of the respective VB structures. In Hubbard model description, the relative weight of the ionic structures depends on the onsite Coulomb repulsion, intersite repulsion and the polarization energy between the cation and the anion. With the two layer A(-1)...B(+1) ONIOM model in my previous email, I hope to guesstimate the polrization energy between the two ions. Thus, the charges on A(-1) should be embedded in the B(+) Hamiltonion, and the charges on (B+) should be embedded in the A(-1) Hamiltonian. But I am not sure if this is meaningful and I don't know how t= o do that. Best regards Roy 2009/11/8 Nicolas Ferr=E9 nicolas.ferre|a|univ-provence.fr < owner-chemistry]=[ccl.net> > > Sent to CCL by: =3D?ISO-8859-1?Q?Nicolas_Ferr=3DE9?=3D [nicolas.ferre.:. > univ-provence.fr] > Sorry, but I don't understand the aim of this discussion. The Oniom metho= d > is a substractive scheme: > > E=3DE(A,high level)-E(A,low level)+E(A+B,low level) > > In the present case: high level=3Dlow level =3D> E=3DE(A+B)!!! Basically = it is a > standard non-Oniom calculation. > > Maybe I miss something, but it seems your calculation is not really > meaningfull ... > > NF > > Morad El-Hendawy m80elhendawy(~)yahoo.com a =E9crit : > > Hey Roy, >> It is easy to model QM/QM by the same method i.e. B3LYP and the same bas= is >> set e.g. 6-31+G** . You can carry out this using Gaussview. I did a simp= le >> example to check that, CH3+NH- it gave a normal termination and it is ri= ght. >> Take care, you have to determine the two centeral atoms in both parts, h= ere >> C+ and N-. As you know there is no pure ionic bond, for example the bond= ing >> between C+ and N- has a partial covalent charecter so you have to set a >> suitable distance between two center, here for example 1.5 Ang. Please a= fter >> you succeed in your calculation, let us know how to overcome difficultie= s >> faced you. >> Good luck, >> >> >> ************************************************************************= **************************** >> *Morad M. El-Hendawy* >> >> >> ************************************************************************= **************************** >> ** *If you want a happy life, do four things:* >> ** *1- Contemplate and be thankful, >> 2- The past is gone forever, >> 3- Today all that you have, >> 4- Leave the future alone until it come. * >> >> ************************************************************************= ********************************************* >> ** >> >> --- On *Sun, 11/8/09, Mahmoud A. A. Ibrahim m.ibrahim1982:-:yahoo.com/> ccl.net>/* wrote: >> >> >> From: Mahmoud A. A. Ibrahim m.ibrahim1982:-:yahoo.com >> >> Subject: CCL: ONIOM calculations >> To: "El-Hendawy, Morad Metwally " >> Date: Sunday, November 8, 2009, 3:41 PM >> >> Dear Roy >> Let's declear some points here: >> Is there a difference between treating your system as two QM-B3LYP >> layers and as one QM-B3LYP layer? in other words, what is the >> difference between QM(B3LYP):QM(B3LYP) and QM(B3LYP) for all the >> system. As I believe, in general speaking, they are the same, but in >> your case, you specify that part A has a charge of a unit value and >> part B has a unit value of charge, and during optimization, each >> part's charge will change with keeping its overall charge unity. >> i.e. say, A's charge -1 and B's charge +1, so after optimization, >> A's charge will be -1 and B's will be +1, but in case of using only >> one QM(B3LYP) for the whole system, in this case, optimization will >> lead to an overall charge of 0 without any limitation on keeping A's >> charge equals to -1 and B's charge equal to +1. >> Roy, is it chemically right to make a limitation on the charge of >> one part of your system? charge is a big challeng. Take care!!! >> Roy, I don't know exactly what are you going to do, but have a look >> on Charge Keyword and R.E.D. program, they may open new thinking >> ways for you. >> Sincerely; >> M. Ibrahim >> Mahmoud A. A. Ibrahim >> Current Address >> School of Chemistry, University of Manchester, >> Oxford Road, Manchester, M13 9PL, United Kingdom. >> >> Home Address >> Chemistry Department, Faculty of Science, >> Minia University, >> Minia 61519,Egypt. >> >> Contact Information >> Email: m.ibrahim#,#compchem.net >> Email: m.ibrahim1982#,#yahoo.com >> Website: www.compchem.net >> Fax No.: +20862342601 >> >> >> --- On *Sun, 11/8/09, Green Power powergreen^-^gmail.com >> //* wrote: >> >> >> From: Green Power powergreen^-^gmail.com > ccl.net> >> Subject: CCL: ONIOM calculations >> To: "Ibrahim, Mahmoud A. A. " >> Date: Sunday, November 8, 2009, 9:15 AM >> >> Dear All, >> >> Can I have a question about two layer ONIOM calculations. For a >> A(-)...B(+) system, I want to learn how the negtive charged A(-) >> is polarized by the positive charged B(+). I would like to know >> whether it is meaningfull to use the same theory levels, say >> B3LYP, for the two layers. This seems to me like a QM:QM model, >> instead of QM:MM which seems more meaningfull to me, Your >> valuable comments and suggestions are highly appriciated. >> >> Roy >> >> >> >> > > -- > Nicolas Ferre' > Laboratoire Chimie Provence > Universite' de Provence - France > Tel: +33 491282733 > http://sites.univ-provence.fr/lcp-ct > > > > -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > --00c09fa217a7f1e40a0477e2a198 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Mahmoud, Morad and Nicolas,

First, thank you for your comments.= Maybe I should describe more question more clearly. In a VB model, a diato= mic bond can be simply described by spin paring, A-B, A(-)-B(+) and A(+)-B(= -1). In VB picture, we can easily learn the relative weight of the respecti= ve VB structures. In Hubbard model description, the relative weight of the = ionic=A0 structures depends on the onsite Coulomb=A0 repulsion, intersite r= epulsion and the polarization energy between the cation and the anion. With= the two layer A(-1)...B(+1) ONIOM model in my previous email, I hope to gu= esstimate the polrization energy between the two ions. Thus, the charges on= A(-1) should be embedded in the B(+) Hamiltonion, and the charges on (B+) = should be embedded in the A(-1) Hamiltonian. But I am not sure if this is m= eaningful and I don't know how to do that.

Best regards

Roy =A0

2009/11/= 8 Nicolas Ferr=E9 nicolas.ferre|a|univ-= provence.fr <owner-chemistry]=[ccl.net>

Sent to CCL by: =3D?ISO-8859-1?Q?Nicolas_Ferr=3DE9?=3D [nicolas.ferre.:.univ-provence.fr] Sorry, but I don't understand the aim of this discussion. The Oniom met= hod is a substractive scheme:

E=3DE(A,high level)-E(A,low level)+E(A+B,low level)

In the present case: high level=3Dlow level =3D> E=3DE(A+B)!!! Basically= it is a standard non-Oniom calculation.

Maybe I miss something, but it seems your calculation is not really meaning= full ...

NF

Morad El-Hendawy m80elhendawy(~)yahoo.com a =E9crit :

Hey Roy,
It is easy to model QM/QM by the same method i.e. B3LYP and the same basis = set e.g. 6-31+G** . You can carry out this using Gaussview. I did a simple = example to check that, CH3+NH- it gave a normal termination and it is right= . Take care, you have to determine the two centeral atoms in both parts, he= re C+ and N-. As you know there is no pure ionic bond, for example the bond= ing between C+ and N- has a partial covalent charecter so you have to set a= suitable distance between two center, here for example 1.5 Ang. Please aft= er you succeed in your calculation, let us know how to overcome difficultie= s faced you.
Good luck,

***************************************************************************= *************************
*Morad M. El-Hendawy*

***************************************************************************= *************************
** *If you want a happy life, do four things:*
** *1- Contemplate and be thankful,
2- The past is gone forever,
3- Today all that you have,
4- Leave the future alone until it come. *
***************************************************************************= ******************************************
**

--- On *Sun, 11/8/09, Mahmoud A. A. Ibrahim m.ibrahim1982:-:yahoo.com /<owner-chemistry-#-ccl.net>/* wrote:

=A0 =A0From: Mahmoud A. A. Ibrahim m.ibrahim1982:-:yahoo.com
=A0 =A0<owner-chemistry-#-= ccl.net>
=A0 =A0Subject: CCL: ONIOM calculations
=A0 =A0To: "El-Hendawy, Morad Metwally " <m80elhendawy-#-yahoo.com>
=A0 =A0Date: Sunday, November 8, 2009, 3:41 PM

=A0 =A0Dear Roy
=A0 =A0Let's declear some points here:
=A0 =A0Is there a difference between treating your system as two QM-B3LYP<= br> =A0 =A0layers and as one QM-B3LYP layer? in other words, what is the
=A0 =A0difference between QM(B3LYP):QM(B3LYP) and =A0QM(B3LYP) for all the=
=A0 =A0system. As I believe, in general speaking, they are the same, but i= n
=A0 =A0your case, you specify that part A has a charge of a unit value and=
=A0 =A0part B has a unit value of charge, and during optimization, each =A0 =A0part's charge will change with keeping its overall charge unity= .
=A0 =A0i.e. say, A's charge -1 and B's charge +1, so after optimiz= ation,
=A0 =A0A's charge will be -1 and B's will be +1, but in case of us= ing only
=A0 =A0one QM(B3LYP) for the whole system, in this case, optimization will=
=A0 =A0lead to an overall charge of 0 without any limitation on keeping A&= #39;s
=A0 =A0charge equals to -1 and B's charge equal to +1.
=A0 =A0Roy, is it chemically right to make a limitation on the charge of =A0 =A0one part of your system? charge is a big challeng. Take care!!!
=A0 =A0Roy, I don't know exactly what are you going to do, but have a = look
=A0 =A0on Charge Keyword and R.E.D. program, they may open new thinking =A0 =A0ways for you.
=A0 =A0Sincerely;
=A0 =A0M. Ibrahim
=A0 =A0Mahmoud A. A. Ibrahim
=A0 =A0Current Address
=A0 =A0School of Chemistry, University of Manchester,
=A0 =A0Oxford Road, Manchester, M13 9PL, United Kingdom.

=A0 =A0Home Address
=A0 =A0Chemistry Department, Faculty of Science,
=A0 =A0Minia University,
=A0 =A0Minia 61519,Egypt.

=A0 =A0Contact Information
=A0 =A0Email: m.ibrahim#,#compchem.net
=A0 =A0Email: m.ibrahim1982#,#yahoo.com
=A0 =A0Website: www.= compchem.net
=A0 =A0Fax No.: +20862342601

=A0 =A0--- On *Sun, 11/8/09, Green Power powergreen^-^gmail.com
=A0 =A0/<owner-chemistry#,#ccl.net>/* wrote:

=A0 =A0 =A0 =A0From: Green Power powergreen^-^gmail.com <owner-chemistry#,#ccl.net>
=A0 =A0 =A0 =A0Subject: CCL: ONIOM calculations
=A0 =A0 =A0 =A0To: "Ibrahim, Mahmoud A. A. " <m.ibrahim1982#,= #yahoo.com>
=A0 =A0 =A0 =A0Date: Sunday, November 8, 2009, 9:15 AM

=A0 =A0 =A0 =A0Dear All,

=A0 =A0 =A0 =A0Can I have a question about two layer ONIOM calculations. F= or a
=A0 =A0 =A0 =A0A(-)...B(+) system, I want to learn how the negtive charged= A(-)
=A0 =A0 =A0 =A0is polarized by the positive charged B(+). I would like to = know
=A0 =A0 =A0 =A0whether it is meaningfull to use the same theory levels, sa= y
=A0 =A0 =A0 =A0B3LYP, for the two layers. This seems to me like a QM:QM mo= del,
=A0 =A0 =A0 =A0instead of QM:MM which seems more meaningfull to me, Your =A0 =A0 =A0 =A0valuable comments and suggestions are highly appriciated.
=A0 =A0 =A0 =A0Roy

--
Nicolas Ferre'
Laboratoire Chimie Provence
Universite' de Provence - France
Tel: +33 491282733
http://s= ites.univ-provence.fr/lcp-ct

-=3D This is automatically added to each message by the mailing script =3D-=
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--00c09fa217a7f1e40a0477e2a198-- From owner-chemistry@ccl.net Sun Nov 8 18:31:00 2009 From: "Mahmoud A. A. Ibrahim m.ibrahim1982-.-yahoo.com" To: CCL Subject: CCL: ONIOM calculations Message-Id: <-40646-091108163143-18743-2EDJULzJLg2FBYOH1oJFpA[-]server.ccl.net> X-Original-From: "Mahmoud A. A. Ibrahim" Content-Type: multipart/alternative; boundary="0-2140474476-1257715881=:22933" Date: Sun, 8 Nov 2009 13:31:21 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim1982~~yahoo.com] --0-2140474476-1257715881=:22933 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Nicolas Ferr=E9=20 You are absolutely right, Two QM/QM with same bases set job is the same as = one QM job, but this is right in regarding to the Energy. But, regarding to= charge, there is a difference related to making restrains on the overall c= harge of separated layers and the whole system. Do one test job, and compare the charges of the atoms and layers. Sincerely; M. Ibrahim Mahmoud A. A. Ibrahim Current Address School of Chemistry, University of Manchester,=20 Oxford Road, Manchester, M13 9PL, United Kingdom. =20 Home Address =20 Chemistry Department, Faculty of Science,=20 Minia University,=20 Minia 61519,Egypt. Contact Information Email: m.ibrahim(!)compchem.net Email: m.ibrahim1982(!)yahoo.com Website: www.compchem.net Fax No.: +20862342601 =20 --- On Sun, 11/8/09, Nicolas Ferr=E9 nicolas.ferre|a|univ-provence.fr wrote: > From: Nicolas Ferr=E9 nicolas.ferre|a|univ-provence.fr Subject: CCL: ONIOM calculations To: "Ibrahim, Mahmoud A. A. " Date: Sunday, November 8, 2009, 6:24 PM Sent to CCL by: =3D?ISO-8859-1?Q?Nicolas_Ferr=3DE9?=3D [nicolas.ferre.:.uni= v-provence.fr] Sorry, but I don't understand the aim of this discussion. The Oniom method = is a substractive scheme: E=3DE(A,high level)-E(A,low level)+E(A+B,low level) In the present case: high level=3Dlow level =3D> E=3DE(A+B)!!! Basically it= is a standard non-Oniom calculation. Maybe I miss something, but it seems your calculation is not really meaning= full ... NF Morad El-Hendawy m80elhendawy(~)yahoo.com a =E9crit : > Hey Roy, > It is easy to model QM/QM by the same method i.e. B3LYP and the same basi= s set e.g. 6-31+G** . You can carry out this using Gaussview. I did a simpl= e example to check that, CH3+NH- it gave a normal termination and it is rig= ht. Take care, you have to determine the two centeral atoms in both parts, = here C+ and N-. As you know there is no pure ionic bond, for example the bo= nding between C+ and N- has a partial covalent charecter so you have to set= a suitable distance between two center, here for example 1.5 Ang. Please a= fter you succeed in your calculation, let us know how to overcome difficult= ies faced you. > Good luck, >=20 > *************************************************************************= *************************** > *Morad M. El-Hendawy* >=20 > *************************************************************************= *************************** > ** *If you want a happy life, do four things:* > ** *1- Contemplate and be thankful, > 2- The past is gone forever, > 3- Today all that you have, > 4- Leave the future alone until it come. * > *************************************************************************= ******************************************** > ** >=20 > --- On *Sun, 11/8/09, Mahmoud A. A. Ibrahim m.ibrahim1982:-:yahoo.com //* wrote: >=20 >=20 >=A0 =A0=A0=A0From: Mahmoud A. A. Ibrahim m.ibrahim1982:-:yahoo.com >=A0 =A0=A0=A0 >=A0 =A0=A0=A0Subject: CCL: ONIOM calculations >=A0 =A0=A0=A0To: "El-Hendawy, Morad Metwally " >=A0 =A0=A0=A0Date: Sunday, November 8, 2009, 3:41 PM >=20 >=A0 =A0=A0=A0Dear Roy >=A0 =A0=A0=A0Let's declear some points here: >=A0 =A0=A0=A0Is there a difference between treating your system as two QM-= B3LYP >=A0 =A0=A0=A0layers and as one QM-B3LYP layer? in other words, what is the >=A0 =A0=A0=A0difference between QM(B3LYP):QM(B3LYP) and=A0 QM(B3LYP) for a= ll the >=A0 =A0=A0=A0system. As I believe, in general speaking, they are the same,= but in >=A0 =A0=A0=A0your case, you specify that part A has a charge of a unit val= ue and >=A0 =A0=A0=A0part B has a unit value of charge, and during optimization, e= ach >=A0 =A0=A0=A0part's charge will change with keeping its overall charge uni= ty. >=A0 =A0=A0=A0i.e. say, A's charge -1 and B's charge +1, so after optimizat= ion, >=A0 =A0=A0=A0A's charge will be -1 and B's will be +1, but in case of usin= g only >=A0 =A0=A0=A0one QM(B3LYP) for the whole system, in this case, optimizatio= n will >=A0 =A0=A0=A0lead to an overall charge of 0 without any limitation on keep= ing A's >=A0 =A0=A0=A0charge equals to -1 and B's charge equal to +1. >=A0 =A0=A0=A0Roy, is it chemically right to make a limitation on the charg= e of >=A0 =A0=A0=A0one part of your system? charge is a big challeng. Take care!= !! >=A0 =A0=A0=A0Roy, I don't know exactly what are you going to do, but have = a look >=A0 =A0=A0=A0on Charge Keyword and R.E.D. program, they may open new think= ing >=A0 =A0=A0=A0ways for you. >=A0 =A0=A0=A0Sincerely; >=A0 =A0=A0=A0M. Ibrahim >=A0 =A0=A0=A0Mahmoud A. A. Ibrahim >=A0 =A0=A0=A0Current Address >=A0 =A0=A0=A0School of Chemistry, University of Manchester, >=A0 =A0=A0=A0Oxford Road, Manchester, M13 9PL, United Kingdom. >=20 >=A0 =A0=A0=A0Home Address >=A0 =A0=A0=A0Chemistry Department, Faculty of Science, >=A0 =A0=A0=A0Minia University, >=A0 =A0=A0=A0Minia 61519,Egypt. >=20 >=A0 =A0=A0=A0Contact Information >=A0 =A0=A0=A0Email: m.ibrahim#,#compchem.net >=A0 =A0=A0=A0Email: m.ibrahim1982#,#yahoo.com >=A0 =A0=A0=A0Website: www.compchem.net >=A0 =A0=A0=A0Fax No.: +20862342601 >=20 >=20 >=A0 =A0=A0=A0--- On *Sun, 11/8/09, Green Power powergreen^-^gmail.com >=A0 =A0=A0=A0//* wrote: >=20 >=20 >=A0 =A0 =A0 =A0=A0=A0From: Green Power powergreen^-^gmail.com >=A0 =A0 =A0 =A0=A0=A0Subject: CCL: ONIOM calculations >=A0 =A0 =A0 =A0=A0=A0To: "Ibrahim, Mahmoud A. A. " >=A0 =A0 =A0 =A0=A0=A0Date: Sunday, November 8, 2009, 9:15 AM >=20 >=A0 =A0 =A0 =A0=A0=A0Dear All, >=20 >=A0 =A0 =A0 =A0=A0=A0Can I have a question about two layer ONIOM calculati= ons. For a >=A0 =A0 =A0 =A0=A0=A0A(-)...B(+) system, I want to learn how the negtive c= harged A(-) >=A0 =A0 =A0 =A0=A0=A0is polarized by the positive charged B(+). I would li= ke to know >=A0 =A0 =A0 =A0=A0=A0whether it is meaningfull to use the same theory leve= ls, say >=A0 =A0 =A0 =A0=A0=A0B3LYP, for the two layers. This seems to me like a QM= :QM model, >=A0 =A0 =A0 =A0=A0=A0instead of QM:MM which seems more meaningfull to me, = Your >=A0 =A0 =A0 =A0=A0=A0valuable comments and suggestions are highly appricia= ted. >=20 >=A0 =A0 =A0 =A0=A0=A0Roy >=20 >=20 >=20 -- Nicolas Ferre' Laboratoire Chimie Provence Universite' de Provence - France Tel: +33 491282733 http://sites.univ-provence.fr/lcp-ct -=3D This is automatically added to each message by the mailing script =3D-=A0 =A0=A0=A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message=A0 =A0=A0=A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message Subscribe/Unsubscribe:=A0 =A0 =A0 http://www.ccl.net/chemistry/sub_unsub.sh= tmlConferences: http://server.ccl.net/chemistry/a= nnouncements/conferences/=A0 =A0=A0=A0http://www.ccl.net/spammers.txt=0A=0A=0A --0-2140474476-1257715881=:22933 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable

Dear Nicolas Ferr=E9
You are absolutely = right, Two QM/QM with same bases set job is the same as one QM job, but thi= s is right in regarding to the Energy. But, regarding to charge, there is a= difference related to making restrains on the overall charge of separated = layers and the whole system.
Do one test job, and compare the charges of= the atoms and layers.
Sincerely;
M. Ibrahim

Current Address

School of Chemistry,= University of Manchester,
Oxford Road, Manchester, M13 9PL, United Kin= gdom.

= Home Address

Chemistry De= partment, Faculty of Science,
Minia University,
= Minia 61519,Egypt.

Contac= t Information
Email: m.ibrahim(!)compchem.net
Email: m.ibrahim19= 82(!)yahoo.com
Website: www.compchem.net
Fax No.: +208623426= 01

--- On Sun, 11/8/09, Nicolas Ferr=E9= nicolas.ferre|a|univ-provence.fr <owner-chemistry(!)ccl.net> wrote:

From: Nicolas Ferr=E9 nicolas.ferr= e|a|univ-provence.fr <owner-chemistry(!)ccl.net>
Subject: CCL: ONIOM= calculations
To: "Ibrahim, Mahmoud A. A. " <m.ibrahim1982(!)yahoo.com>
Date: Sunday, November 8, 2009, 6:24 PM=

Sent to CCL by: =3D?ISO-8859-1?Q?Nicol= as_Ferr=3DE9?=3D [nicolas.ferre.:.univ-provence.fr]
Sorry, but I don't u= nderstand the aim of this discussion. The Oniom method is a substractive sc= heme:

E=3DE(A,high level)-E(A,low level)+E(A+B,low level)

In = the present case: high level=3Dlow level =3D> E=3DE(A+B)!!! Basically it= is a standard non-Oniom calculation.

Maybe I miss something, but it= seems your calculation is not really meaningfull ...

NF

Mora= d El-Hendawy m80elhendawy(~)yahoo.com a =E9crit :
> Hey Roy,
> = It is easy to model QM/QM by the same method i.e. B3LYP and the same basis = set e.g. 6-31+G** . You can carry out this using Gaussview. I did a simple = example to check that, CH3+NH- it gave a normal termination and it is right= . Take care, you have to determine the two centeral atoms in both parts, he= re C+ and N-. As you know there is no pure ionic bond, for example the bonding betwe= en C+ and N- has a partial covalent charecter so you have to set a suitable= distance between two center, here for example 1.5 Ang. Please after you su= cceed in your calculation, let us know how to overcome difficulties faced y= ou.
> Good luck,
>
> ***********************************= *****************************************************************
> *= Morad M. El-Hendawy*
>
> *************************************= ***************************************************************
> ** = *If you want a happy life, do four things:*
> ** *1- Contemplate and = be thankful,
> 2- The past is gone forever,
> 3- Today all that= you have,
> 4- Leave the future alone until it come. *
> *****= ***************************************************************************= *************************************
> **
>
> --- On *Sun, 11/8/09, Mahmoud A. A. Ibrahim m.ibrahim1982:-:yahoo.com /<= ;owner-chemistry-#-ccl.net>/* wrote:
>
>
> &nb= sp;  From: Mahmoud A. A. Ibrahim m.ibrahim1982:-:yahoo.com
>= ;    <owner-chemistry-#-ccl.net>
> &= nbsp;  Subject: CCL: ONIOM calculations
>   = ; To: "El-Hendawy, Morad Metwally " <m80elhendawy-#-yahoo.com>>    Date: Sunday, November 8, 2009, 3:41 PM
&= gt;
>    Dear Roy
>   &nb= sp;Let's declear some points here:
>    Is there= a difference between treating your system as two QM-B3LYP
> &n= bsp;  layers and as one QM-B3LYP layer? in other words, what is t= he
>    difference between QM(B3LYP):QM(B3LYP) a= nd QM(B3LYP) for all the
>    system. As I believe, in general speaking, they are the = same, but in
>    your case, you specify that pa= rt A has a charge of a unit value and
>    part = B has a unit value of charge, and during optimization, each
> &= nbsp;  part's charge will change with keeping its overall charge = unity.
>    i.e. say, A's charge -1 and B's char= ge +1, so after optimization,
>    A's charge wi= ll be -1 and B's will be +1, but in case of using only
> =   one QM(B3LYP) for the whole system, in this case, optimization = will
>    lead to an overall charge of 0 without= any limitation on keeping A's
>    charge equal= s to -1 and B's charge equal to +1.
>    Roy, is= it chemically right to make a limitation on the charge of
>    one part of your system? charge is a bi= g challeng. Take care!!!
>    Roy, I don't know = exactly what are you going to do, but have a look
>   = ; on Charge Keyword and R.E.D. program, they may open new thinking
= >    ways for you.
>    = Sincerely;
>    M. Ibrahim
> &= nbsp; Mahmoud A. A. Ibrahim
>    Current Ad= dress
>    School of Chemistry, University of Ma= nchester,
>    Oxford Road, Manchester, M13 9PL,= United Kingdom.
>
>    Home Address
&= gt;    Chemistry Department, Faculty of Science,
&g= t;    Minia University,
>   &nbs= p;Minia 61519,Egypt.
>
>    Contact Information
>    Emai= l: m.ibrahim#,#compchem.net
>    Email: m.ibrahi= m1982#,#yahoo.com
>    Website: www.compchem.net=
>    Fax No.: +20862342601
>
> >    --- On *Sun, 11/8/09, Green Power powergreen^= -^gmail.com
>    /<owner-chemistry#,#ccl.net&= gt;/* wrote:
>
>
>   &nbs= p;From: Green Power powergreen^-^gmail.com <owner-chemistry#,#ccl.net>= ;
>    Subject: CCL: ONIOM calcula= tions
>    To: "Ibrahim, Mahmoud A= . A. " <m.ibrahim1982#,#yahoo.com>
> =   Date: Sunday, November 8, 2009, 9:15 AM
>
> =    Dear All,
>
>    Can I have a question about two layer ONIO= M calculations. For a
>    A(-)...= B(+) system, I want to learn how the negtive charged A(-)
> &nb= sp;    is polarized by the positive charged B(+). I w= ould like to know
>    whether it = is meaningfull to use the same theory levels, say
> &nbs= p;    B3LYP, for the two layers. This seems to me like a QM:= QM model,
>    instead of QM:MM wh= ich seems more meaningfull to me, Your
> &n= bsp; valuable comments and suggestions are highly appriciated.
>=
>    Roy
>
>
&g= t;

-- Nicolas Ferre'
Laboratoire Chimie Provence
Universi= te' de Provence - France
Tel: +33 491282733
http://sit= es.univ-provence.fr/lcp-ct

-=3D This is automatically ad= ded to each message by the mailing script =3D-
To recover the email addr= ess of the author of the message, please change
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=0A=0A --0-2140474476-1257715881=:22933-- From owner-chemistry@ccl.net Sun Nov 8 19:07:00 2009 From: "Mahmoud A. A. Ibrahim m.ibrahim1982-.-yahoo.com" To: CCL Subject: CCL:G: AMBER 94 Atom Type in MOE and Gaussian 03/09 Message-Id: <-40647-091108161048-8975-yglsWpol044Hqvb4SsgMYA__server.ccl.net> X-Original-From: "Mahmoud A. A. Ibrahim" Content-Type: multipart/alternative; boundary="0-1121658070-1257714637=:78353" Date: Sun, 8 Nov 2009 13:10:37 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim1982###yahoo.com] --0-1121658070-1257714637=:78353 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Morad I am so sorry, I was in a long vacation in home, so I will start to=0Areply= on your enquiry here on CCL to give a chance to anybody else to=0Aread=0Am= y reply and add any comment: H1 and HP are very similar hydrogen atom types H1: H aliph. bond. to C with 1 electrwd. group HP: H bonded to C next to positively charged group (e.g. C next to NH3+ of = lysine) By the way, all force fields parameters for these two atom types are simila= r. For example: CT-HP=A0 340.0=A0=A0=A0 1.090=A0=A0=A0=A0=A0=A0=A0=20 CT-H1=A0 340.0=A0=A0=A0 1.090 CT-CT-H1=A0=A0=A0 50.0=A0=A0=A0=A0=A0 109.50 CT-CT-HP=A0=A0=A0 50.0=A0=A0=A0=A0=A0 109.50 and so on. So, as I believe it is not a big problem. Sincerely; M.=0A Ibrahim Mahmoud A. A. Ibrahim Current Address School of Chemistry, University of Manchester,=20 Oxford Road, Manchester, M13 9PL, United Kingdom. =20 Home Address =20 Chemistry Department, Faculty of Science,=20 Minia University,=20 Minia 61519,Egypt. Contact Information Email: m.ibrahim .. compchem.net Email: m.ibrahim1982 .. yahoo.com Website: www.compchem.net =0A Fax No.: +20862342601 =20 --- On Tue, 10/20/09, Morad M El-Hendawy M80elhendawy{:}yahoo.com wrote: > From: Morad M El-Hendawy M80elhendawy{:}yahoo.com Subject: CCL:G: AMBER 94 Atom Type in MOE and Gaussian 03/09 To: "Ibrahim, Mahmoud A. A. " Date: Tuesday, October 20, 2009, 3:07 PM Sent to CCL by: "Morad M El-Hendawy" [M80elhendawy=3Dyahoo.com] Hello CCLers! I prepared an input file of the active site of certain protein to do QM/MM;= MM=3DAMBER94 using ONIOM Gaussian 03. When compare the atom types in both = cases I found there some differences, for example, a hydrogen atom has atom= type=3D HP in MOE and that of Gaussian03 is H1. So, am confused for that. = I wonder=0A if there is Any expertise body can give a clear cut for this co= nfusion. Best regards, Morad M EL-Hendawy IRELAND -=3D This is automatically added to each message by the mailing script =3D-=A0 =A0 =A0=A0 =A0 =A0Subscribe/Unsubscribe:=20 =A0 =A0 =A0Job: http://www.ccl.net/jobs=20=A0 =A0 =A0=0A=0A=0A --0-1121658070-1257714637=:78353 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable

Dear Morad
I am s= o sorry, I was in a long vacation in home, so I will start to=0Areply on yo= ur enquiry here on CCL to give a chance to anybody else to=0Aread=0Amy repl= y and add any comment:
H1 and HP are very similar hydrogen atom typesH1: H aliph. bond. to C with 1 electrwd. group
HP: H bonded to C next t= o positively charged group (e.g. C next to NH3+ of lysine)
By the way, a= ll force fields parameters for these two atom types are similar.
For exa= mple:
CT-HP 340.0    1.090    &= nbsp;
CT-H1 340.0    1.090

CT-C= T-H1    50.0      109.50
CT-CT-H= P    50.0      109.50

and so= on. So, as I believe it is not a big problem.
Sincerely;
M.=0A Ibrah= im

Mahmoud A. A. Ibrahim

Current = Address

School of Chemistry, University of Manchester,
Oxford Road, Manchest= er, M13 9PL, United Kingdom.

Home Address =

Chemistry Department, Faculty of Science,
= Minia University,
Minia 61519,Egypt.

Contact Information
Email: m.ibrahi= m .. compchem.net
Email: m.ibrahim1982 .. yahoo.com
Website: www.compchem.n= et
=0A Fax No.: +20862342601

= --- On Tue, 10/20/09, Morad M El-Hendawy M80elhendawy{:}yahoo.com <= ;owner-chemistry .. ccl.net> wrote:

From: Morad M El-Hendawy M80elhendawy{:}yahoo.com <owner-chemistry .. ccl.= net>
Subject: CCL:G: AMBER 94 Atom Type in MOE and Gaussian 03/09
= To: "Ibrahim, Mahmoud A. A. " <m.ibrahim1982 .. yahoo.com>
Da= te: Tuesday, October 20, 2009, 3:07 PM

= Sent to CCL by: "Morad M El-Hendawy" [M80elhendawy=3Dyahoo.com]
Hello CC= Lers!
I prepared an input file of the active site of certain protein to = do QM/MM; MM=3DAMBER94 using ONIOM Gaussian 03. When compare the atom types= in both cases I found there some differences, for example, a hydrogen atom= has atom type=3D HP in MOE and that of Gaussian03 is H1. So, am confused f= or that. I wonder=0A if there is Any expertise body can give a clear cut fo= r this confusion.
Best regards,
Morad M EL-Hendawy
IRELAND

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