From owner-chemistry@ccl.net Wed Nov 18 12:51:01 2009 From: "Morad El-Hendawy m80elhendawy]^[yahoo.com" To: CCL Subject: CCL:G: Partial charges created by Gaussview Message-Id: <-40701-091118124931-10326-21JROXcJaCUQiwFwz0f/EA-x-server.ccl.net> X-Original-From: Morad El-Hendawy Content-Type: multipart/alternative; boundary="0-1883863568-1258566559=:52519" Date: Wed, 18 Nov 2009 09:49:19 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Morad El-Hendawy [m80elhendawy||yahoo.com] --0-1883863568-1258566559=:52519 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hey every body, I inquires about the reliabilty of partial charges created by Gaussview in = order to do MM calculation using AMBER (Gaussian 09) for a certain protien.= When I compared between the created partial charges of this protien using = Gaussview and MOE (molecular Operating Enviroment) using the same force fie= ld (AMBER94), I found the partial charge in both cases are the same except = for the first residue atoms (ALA)=A0 which is act as N-terminous as the fol= lowing: =0A=0A=0A=0A=0A =0A =0A Atom No=0A =0A =0A Atom symbol=0A =0A =0A A= MBER type=0A =0A =0A GaussView=0A Partial charges=0A =0A =0A MOE=0A = Partial charges=0A =0A =0A AMBER Fragment=0A =0A =0A Chain=0A =0A = =0A =0A =0A 1=0A =0A =0A N=0A =0A =0A N3=0A =0A =0A 0.1414000=0A= =0A =0A -0.416=0A =0A =0A Ala_Nt=0A =0A =0A A=0A =0A =0A =0A = =0A 2=0A =0A =0A H=0A =0A =0A H=0A =0A =0A 0.1997000=0A =0A =0A= =A00.272=0A =0A =0A Ala_Nt=0A =0A =0A A=0A =0A =0A =0A =0A 3=0A = =0A =0A H=0A =0A =0A H=0A =0A =0A 0.1997000=0A =0A =0A =A00.272= =0A =0A =0A Ala_Nt=0A =0A =0A A=0A =0A =0A =0A =0A 4=0A =0A =0A = H=0A =0A =0A H=0A =0A =0A 0.1997000=0A =0A =0A =A00.272=0A =0A = =0A Ala_Nt=0A =0A =0A A=0A =0A =0A =0A =0A 5=0A =0A =0A C=0A =0A= =0A CT=0A =0A =0A 0.0962000=0A =0A =0A =A00.034=0A =0A =0A Ala_= Nt=0A =0A =0A A=0A =0A =0A =0A =0A 6=0A =0A =0A H=0A =0A =0A HP= =0A =0A =0A 0.0889000=0A =0A =0A =A00.082=0A =0A =0A Ala_Nt=0A = =0A =0A A=0A =0A =0A =0A =0A 7=0A =0A =0A C=0A =0A =0A C=0A =0A= =0A 0.6163000=0A =0A =0A =A00.597=0A =0A =0A Ala_Nt=0A =0A =0A = A=0A =0A =0A =0A =0A 8=0A =0A =0A O=0A =0A =0A O=0A =0A =0A -0.= 5722000=0A =0A =0A -0.568=0A =0A =0A Ala_Nt=0A =0A =0A A=0A =0A = =0A =0A =0A 9=0A =0A =0A C=0A =0A =0A CT=0A =0A =0A -0.0597000= =0A =0A =0A -0.183=0A =0A =0A Ala_Nt=0A =0A =0A A=0A =0A =0A =0A = =0A 10=0A =0A =0A H=0A =0A =0A HC=0A =0A =0A 0.0300000=0A =0A = =0A =A00.060=0A =0A =0A Ala_Nt=0A =0A =0A A=0A =0A =0A =0A =0A 11= =0A =0A =0A H=0A =0A =0A HC=0A =0A =0A 0.0300000=0A =0A =0A =A0= 0.060=0A =0A =0A Ala_Nt=0A =0A =0A A=0A =0A =0A =0A =0A 12=0A =0A= =0A H=0A =0A =0A HC=0A =0A =0A 0.0300000=0A =0A =0A =A00.060=0A= =0A =0A Ala_Nt=0A =0A =0A A=0A =0A =0A =0A =0A 13=0A =0A =0A N= =0A =0A =0A N=0A =0A =0A -0.4157000=0A =0A =0A -0.416=0A =0A =0A= Ser=0A =0A =0A A=0A =0A =0A =0A =0A 14=0A =0A =0A H=0A =0A =0A= H=0A =0A =0A 0.2719000=0A =0A =0A =A00.272=0A =0A =0A Ser=0A = =0A =0A A=0A =0A =0A =0A =0A 15=0A =0A =0A C=0A =0A =0A CT=0A = =0A =0A -0.0249000=0A =0A =0A -0.025=0A =0A =0A Ser=0A =0A =0A A= =0A =0A =0A =0A =0A 16=0A =0A =0A H=0A =0A =0A H1=0A =0A =0A 0.= 0843000=0A =0A =0A =A00.084=0A =0A =0A Ser=0A =0A =0A A=0A =0A = =0A =0A =0A 17=0A =0A =0A C=0A =0A =0A C=0A =0A =0A 0.5973000=0A= =0A =0A =A00.597=0A =0A =0A Ser=0A =0A =0A A=0A =0A =0A =0A =0A= 18=0A =0A =0A O=0A =0A =0A O=0A =0A =0A -0.5679000=0A =0A =0A = -0.568=0A =0A =0A Ser=0A =0A =0A A=0A =0A =0A =0A =0A 19=0A =0A = =0A C=0A =0A =0A CT=0A =0A =0A 0.2117000=0A =0A =0A =A00.212=0A = =0A =0A Ser=0A =0A =0A A=0A =0A =0A =0A =0A 20=0A =0A =0A H=0A = =0A =0A H1=0A =0A =0A 0.0352000=0A =0A =0A =A00.035=0A =0A =0A = Ser=0A =0A =0A A=0A =0A =0A =0A =0A 21=0A =0A =0A H=0A =0A =0A = H1=0A =0A =0A 0.0352000=0A =0A =0A =A00.035=0A =0A =0A Ser=0A =0A= =0A A=0A =0A =0A =0A =0A 22=0A =0A =0A O=0A =0A =0A OH=0A =0A = =0A -0.6546000=0A =0A =0A -0.655=0A =0A =0A Ser=0A =0A =0A A=0A = =0A =0A=0A=0A =A0This table includes the partial charges of first two residues (AlA & Ser= ) of protien. As seen, the partial charges of atoms of Ser in both cases ar= e the same but they are different in case these of ALA. My question how to know which program creating partial charges for ALA atom= s is right?? Best regards ***************************************************************************= ***********************Morad M. El-HendawyIRELAND ***************************************************************************= ***********************=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********************************= ***************************************************************************= ********=0A=0A=0A --0-1883863568-1258566559=:52519 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Hey every body,
I inquires about the relia= bilty of partial charges created by Gaussview in order to do MM calculation= using AMBER (Gaussian 09) for a certain protien. When I compared between t= he created partial charges of this protien using Gaussview and MOE (molecul= ar Operating Enviroment) using the same force field (AMBER94), I found the = partial charge in both cases are the same except for the first residue atom= s (ALA)  which is act as N-terminous as the following:

<= link rel=3D"File-List" href=3D"file:///C:%5CDOCUME%7E1%5Cmorad%5CLOCALS%7E1= %5CTemp%5Cmsohtml1%5C01%5Cclip_filelist.xml">=0A=0A=0A =0A =0A =0A = =0A =0A =0A = =0A =0A =0A =0A =0A =0A =0A =0A =0A =0A =0A =0A = =0A =0A =0A =0A =0A =0A =0A =0A =0A =0A =0A =0A =0A =0A =0A =0A =0A =0A =0A =0A =0A =0A =0A =0A= =0A =0A =0A =0A =0A =0A =0A= =0A =0A =0A = =0A =0A =0A =0A =0A = =0A

Ala_Nt

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

CT

=0A =0A =0A =0A =0A =0A =0A =0A =0A =0A =0A =0A =0A =0A =0A =0A =0A =0A =0A = =0A =0A =0A =0A =0A =0A =0A =0A =0A =0A =0A =0A= =0A =0A =0A = =0A =0A =0A =0A =0A =0A =0A =0A =0A =0A =0A =0A =0A =0A =0A =0A =0A =0A =0A =0A =0A =0A =0A =0A = =0A =0A =0A =0A <= td style=3D"border-style: none solid solid none; border-color: -moz-use-tex= t-color windowtext windowtext -moz-use-text-color; border-width: medium 1pt= 1pt medium; padding: 0cm 5.4pt; width: 53.5pt;" valign=3D"top" width=3D"71= ">=0A

H1

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

A

=0A =0A =0A<= /table>=0A=0A
 This table includes the partial charges of first two= residues (AlA & Ser) of protien. As seen, the partial charges of atoms= of Ser in both cases are the same but they are different in case these of = ALA.
My question how to know which program creating partial charges for = ALA atoms is right??
Best regards

*****************************************= *********************************************************
Morad M. E= l-Hendawy
IRELAND
***********************************************************= ***************************************
<= font style=3D"background-color: rgb(230, 230, 230);" color=3D"#00407f"> If you want a happy life, do four things:
 
1- Contemplate and be thankful,=
2- The past is go= ne forever,
3- Today all that you have,
4- Leave the future alone until it come. 
*****************= ***************************************************************************= ***********************
3D""
=0A

Atom No

=0A 		=0A

Atom symbol

=0A 		=0A

AMBER type

=0A 		= =0A

GaussView

=0A

Partial = charges

=0A 		=0A

MOE

=0A

Partial charges

=0A 		=0A

AMBER Fragment

=0A 		=0A=

Chain=0A

=0A

1=

=0A 		=0A

N<= /p>=0A

=0A

N3

=0A =0A 		=0A

0.141= 4000

=0A 		=0A

-0.416

=0A 		=0A =

Ala_Nt

=0A 		=0A

A

=0A
=0A

2

=0A 		=0A

H

=0A 		=0A

H

=0A 		=0A

0.1997000

=0A 		=0A =

&nbs= p;0.272

=0A 		=0A

Ala_Nt

=0A 		=0A

A=

=0A
=0A

3

=0A 		=0A

H

=0A 		=0A

H=

=0A 		=0A

0.1997000

=0A 		=0A

 0.272

=0A 		=0A

Ala_Nt

=0A 		=0A

A

= =0A
=0A

4<= o:p>

=0A 		=0A

H=0A

=0A

H

=0A =0A 		=0A

0.1997= 000

=0A 		=0A

 0.272

=0A 		=0A

Ala_Nt

= =0A 		=0A

A

=0A
=0A

5=0A

=0A

C

=0A =0A 		=0A

CT

=0A 		= =0A

0.0962000

=0A 		=0A

 0.034

=0A = 		=0A

Ala_Nt

=0A 		=0A

A

=0A
=0A

6

=0A 		=0A

H

=0A 		=0A =

HP

=0A 		=0A

0.0889000=0A

=0A

=  0.082

=0A 		=0A <= p class=3D"MsoNormal">A

=0A
=0A

7

=0A 		=0A =

C

=0A 		=0A

C

=0A 		=0A

= 0.6163000

=0A 		=0A

 0.597

=0A 		=0A

Ala_Nt

=0A 		=0A

A

=0A
=0A

8

=0A 		=0A

O

=0A 		=0A

O

=0A 		=0A

-0.5722000

=0A 		=0A

-0.568

= =0A 		=0A

Ala_Nt

=0A =0A 		=0A

A

=0A
=0A =

9

=0A = 		=0A

C

=0A 		=0A

-0.0597000

=0A 		=0A

-0.183

=0A 		=0A

Ala_Nt

=0A 		=0A

A

=0A
=0A

10

=0A 		=0A

H=

=0A 		=0A

HC<= /p>=0A

=0A

0.0300000

=0A 		=0A

 0.060

=0A 		=0A

Ala_Nt=

=0A 		=0A

A

=0A=
=0A

11

=0A 		=0A

H

= =0A 		=0A

HC

=0A 		=0A

0.03000= 00

=0A 		=0A

 0.060

=0A 		=0A

Ala_Nt

=0A= 		=0A

A

=0A
= =0A

12=0A

=0A

H

=0A =0A 		=0A

HC

=0A 		= =0A

0.0300000

=0A 		=0A

 0.060

=0A = 		=0A

Ala_Nt

=0A 		=0A

A

=0A
=0A

13

=0A 		=0A

N

=0A 		=0A =

N

=0A 		=0A

-0.4157000=

=0A 		=0A

-0.416

=0A 		=0A

Ser

=0A 		=0A

A

=0A
=0A

14

=0A 		=0A

H

=0A 		=0A

H

=0A 		=0A

0.2719000

=0A 		=0A

 0.272

=0A 		=0A

Ser

=0A 		=0A

A=

=0A
=0A

15

=0A 		=0A

C

=0A 		=0A

CT=0A

=0A

-0.0249000

=0A 		=0A

-0.025=

=0A 		=0A

Ser

=0A =0A 		=0A

A

=0A
=0A =

16

=0A = 		=0A

H

=0A 		=0A

0.0843000

=0A 		=0A

 0.084

= =0A 		=0A

Ser

=0A 		=0A

A

=0A
=0A

17

=0A =0A 		=0A

C

=0A 		= =0A

C

=0A 		=0A

0.5973000

=0A 		=0A

 0.597

=0A = 		=0A

Ser

=0A 		=0A

A

=0A
=0A

18

=0A 		=0A

O

=0A 		=0A =

O

=0A 		=0A

-0.5679000=

=0A 		=0A

-0.568

=0A 		=0A

Ser

=0A 		=0A

A

=0A
=0A

19

=0A 		=0A

C

=0A 		=0A

CT

=0A 		=0A

0.2117000

=0A 		=0A

 0.212

=0A 		=0A

Ser

=0A 		=0A

A

=0A
=0A

20

=0A 		=0A

H<= o:p>

=0A 		=0A

H1=0A

=0A

0.0352000

=0A 		=0A

 0= .035

=0A 		=0A

Ser

=0A 		=0A

A

=0A
=0A

21

=0A 		=0A

H

=0A 		=0A

H1

= =0A 		=0A

0.0352000

=0A 		=0A

 0.03= 5

=0A 		=0A

Se= r

=0A 		=0A

A<= /p>=0A

=0A

22

=0A 		=0A

O

=0A 		=0A

OH

=0A <= /td>=0A 		=0A

-= 0.6546000

=0A 		=0A

-0.655

=0A =0A 		=0A

Ser

=0A

=0A=0A --0-1883863568-1258566559=:52519-- From owner-chemistry@ccl.net Wed Nov 18 13:26:00 2009 From: "Peter M Burger burger~~chemie.uni-hamburg.de" To: CCL Subject: CCL:G: G IRC run goes in same direction Message-Id: <-40702-091118130625-17813-4bm8XK9cdcXkUxY/HZw0zw _ server.ccl.net> X-Original-From: "Peter M Burger" Date: Wed, 18 Nov 2009 13:06:21 -0500 Sent to CCL by: "Peter M Burger" [burger**chemie.uni-hamburg.de] Hello, I noticed that the following question was asked before here but did not find a conclusive answer. So what can be done if an IRC run in g03 goes in the same direction for both the reverse and forward keywords? Regards Peter From owner-chemistry@ccl.net Wed Nov 18 14:00:01 2009 From: "Demetrios Xenides xenides(~)uop.gr" To: CCL Subject: CCL: fingerprints (or bitstrings) of compounds Message-Id: <-40703-091118131707-23178-Tstdanudpsw4nN3dfAn4kw(0)server.ccl.net> X-Original-From: "Demetrios Xenides" Date: Wed, 18 Nov 2009 13:17:03 -0500 Sent to CCL by: "Demetrios Xenides" [xenides^-^uop.gr] Hi CCL community!!! I would greatly appreciate your kind assistance in the following: Is there any possible (preferably not commercial) way to convert smile names to bit strings? It would be also nice if you can point to some relevant (online) data. Best Regards, Demetrios From owner-chemistry@ccl.net Wed Nov 18 14:35:00 2009 From: "emendez _ quimica.uh.cu" To: CCL Subject: CCL: basis set for gold surfaces Message-Id: <-40704-091117171817-5956-fMV1NfEcrooZpTS2KJuM4g[-]server.ccl.net> X-Original-From: emendez^quimica.uh.cu Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Tue, 17 Nov 2009 15:53:49 -0500 MIME-Version: 1.0 Sent to CCL by: emendez(-)quimica.uh.cu Hi I´m trying to run a DFT simulation on an Au(111) surface and I need a basis set of good performance for my system. Would anyone recommend me a good one? Thank´s in advance, Enrique Mendez From owner-chemistry@ccl.net Wed Nov 18 15:11:01 2009 From: "Wolf Ihlenfeldt wdi]|[xemistry.com" To: CCL Subject: CCL: fingerprints (or bitstrings) of compounds Message-Id: <-40705-091118144716-30232-/7FbA/XPK+YXQN80/Q18LA .. server.ccl.net> X-Original-From: Wolf Ihlenfeldt Content-Type: multipart/alternative; boundary=0016e6d7e4e1b408d20478aa8154 Date: Wed, 18 Nov 2009 20:47:02 +0100 MIME-Version: 1.0 Sent to CCL by: Wolf Ihlenfeldt [wdi/a\xemistry.com] --0016e6d7e4e1b408d20478aa8154 Content-Type: text/plain; charset=UTF-8 Use the Cactvs toolkit (www.xemistry.com, free for academia). A small sample script: ---- prop setparam E_SCREEN extended 2 molfile loop "your_file.smi" eh { puts [ens get $eh E_SCREEN] } --- This will give you the PubChem screen bits (used for substructure and similarity search). Their definition can be found at the PubChem Web site. This is a fragment-based set, if you prefer a hashed path scheme, you can use E_PATH_FINGERPRINT. Both E_SCREEN and E_PATH_FINGERPRINT have additional parameters for fine-tuning. On Wed, Nov 18, 2009 at 7:17 PM, Demetrios Xenides xenides(~)uop.gr < owner-chemistry!^!ccl.net> wrote: > > Sent to CCL by: "Demetrios Xenides" [xenides^-^uop.gr] > Hi CCL community!!! > > I would greatly appreciate your kind assistance in the following: > > Is there any possible (preferably not commercial) way to convert smile > names to bit strings? It would be also nice if you can point to some > relevant (online) data. > > Best Regards, > Demetrios> > > --0016e6d7e4e1b408d20478aa8154 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Use the Cactvs toolkit (www.xemistry.com, free for academia).
=C2=A0
A small sample script:
=C2=A0
----
prop setparam E_SCREEN extended 2
molfile loop "your_file.smi" eh {
=C2=A0=C2=A0 puts [ens get $eh E_SCREEN]
}
---
=C2=A0
This will give you the PubChem screen bits (used for substructure and = similarity search). Their definition can be found at the PubChem Web site. = This is a fragment-based set, if you prefer a hashed path scheme, you can u= se E_PATH_FINGERPRINT. Both E_SCREEN and E_PATH_FINGERPRINT have additional= parameters for fine-tuning.


=C2=A0
On Wed, Nov 18, 2009 at 7:17 PM, Demetrios Xenid= es xenides(~)uop.gr <owner-chemistry!^!ccl.net> wrote:

Sent to CCL by: "Demetr= ios =C2=A0Xenides" [xenides^-^uop.gr]
Hi CCL community!!!

I would greatly appreciate your kind assistance = in the following:

Is there any possible (preferably not commercial) = way to convert smile names to bit strings? It would be also nice if you can= point to some relevant (online) data.

Best Regards,
Demetrios



-=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
the strange characters o= n the top line to the !^! sign. You can also
E-mail to subs= cribers: CHEMISTRY!^!ccl.net or use:=
=C2=A0 =C2=A0 =C2=A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message<= /a>

E-mail to administrators: = CHEMISTRY-REQUEST!^!ccl.net or use
=C2=A0 =C2=A0 =C2=A0http://www.c= cl.net/cgi-bin/ccl/send_ccl_message

Subscribe/Unsubscribe:
=C2=A0 =C2=A0 =C2=A0http://www.ccl.net/chemis= try/sub_unsub.shtml

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

Job: http://www.c= cl.net/jobs
Conferences: http://server.ccl.net/chemist= ry/announcements/conferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.sht= ml
=C2= =A0 =C2=A0 =C2=A0http://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/


--0016e6d7e4e1b408d20478aa8154-- From owner-chemistry@ccl.net Wed Nov 18 15:51:01 2009 From: "Mahmoud A. A. Ibrahim m.ibrahim1982,+,yahoo.com" To: CCL Subject: CCL:G: Partial charges created by Gaussview Message-Id: <-40706-091118151515-18919-C3FziTqo1U+7nPBTpmCRXg],[server.ccl.net> X-Original-From: "Mahmoud A. A. Ibrahim" Content-Type: multipart/alternative; boundary="0-48102598-1258575302=:98383" Date: Wed, 18 Nov 2009 12:15:02 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim1982 : yahoo.com] --0-48102598-1258575302=:98383 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Morad Regarding to your question, Partial Charges generated using GaussView are t= he correct ones, they are the same exactly as in the AMBER implemented valu= es (ALA N-terminus; called NALA residue in AMBER). About MOE, it has generated ALA charges considering ALA as NON-terminus ALA= residue (i.e. as ALA). This is where the difference come from. May be this= error returned to an error in defining your system using MOE (your input f= ile). Sorry, but I don't have much experience in using MOE to know why it h= appened. P.S. my private email was dealing with NON-Standard Residue. 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/a\compchem.net Email: m.ibrahim1982/a\yahoo.com Website: www.compchem.net Fax No.: +20862342601 =20 --- On Wed, 11/18/09, Morad El-Hendawy m80elhendawy]^[yahoo.com wrote: > From: Morad El-Hendawy m80elhendawy]^[yahoo.com Subject: CCL:G: Partial charges created by Gaussview To: "Ibrahim, Mahmoud A. A. " Date: Wednesday, November 18, 2009, 5:49 PM Hey every body, I inquires about the reliabilty of partial charges created by Gaussview in = order to do MM calculation using AMBER (Gaussian 09) for a certain protien.= When I compared between the created partial charges of this protien using = Gaussview and MOE (molecular Operating Enviroment) using the same force fie= ld (AMBER94), I found the partial charge in both cases are the same except = for the first residue atoms (ALA)=A0 which is act as N-terminous as the fol= lowing: =0A=0A=0A=0A=0A =0A =0A Atom No =0A =0A =0A Atom symbol =0A =0A =0A = AMBER type =0A =0A =0A GaussView =0A Partial charges =0A =0A =0A MO= E =0A Partial charges =0A =0A =0A AMBER Fragment =0A =0A =0A Chain = =0A =0A =0A =0A =0A 1 =0A =0A =0A N =0A =0A =0A N3 =0A =0A =0A = 0.1414000 =0A =0A =0A -0.416 =0A =0A =0A Ala_Nt =0A =0A =0A A =0A = =0A =0A =0A =0A 2 =0A =0A =0A H =0A =0A =0A H =0A =0A =0A 0.199= 7000 =0A =0A =0A =A00.272 =0A =0A =0A Ala_Nt =0A =0A =0A A =0A = =0A =0A =0A =0A 3 =0A =0A =0A H =0A =0A =0A H =0A =0A =0A 0.1997= 000 =0A =0A =0A =A00.272 =0A =0A =0A Ala_Nt =0A =0A =0A A =0A =0A= =0A =0A =0A 4 =0A =0A =0A H =0A =0A =0A H =0A =0A =0A 0.1997000= =0A =0A =0A =A00.272 =0A =0A =0A Ala_Nt =0A =0A =0A A =0A =0A = =0A =0A =0A 5 =0A =0A =0A C =0A =0A =0A CT =0A =0A =0A 0.0962000= =0A =0A =0A =A00.034 =0A =0A =0A Ala_Nt =0A =0A =0A A =0A =0A = =0A =0A =0A 6 =0A =0A =0A H =0A =0A =0A HP =0A =0A =0A 0.0889000= =0A =0A =0A =A00.082 =0A =0A =0A Ala_Nt =0A =0A =0A A =0A =0A = =0A =0A =0A 7 =0A =0A =0A C =0A =0A =0A C =0A =0A =0A 0.6163000 = =0A =0A =0A =A00.597 =0A =0A =0A Ala_Nt =0A =0A =0A A =0A =0A =0A= =0A =0A 8 =0A =0A =0A O =0A =0A =0A O =0A =0A =0A -0.5722000 = =0A =0A =0A -0.568 =0A =0A =0A Ala_Nt =0A =0A =0A A =0A =0A =0A = =0A =0A 9 =0A =0A =0A C =0A =0A =0A CT =0A =0A =0A -0.0597000 = =0A =0A =0A -0.183 =0A =0A =0A Ala_Nt =0A =0A =0A A =0A =0A =0A = =0A =0A 10 =0A =0A =0A H =0A =0A =0A HC =0A =0A =0A 0.0300000 = =0A =0A =0A =A00.060 =0A =0A =0A Ala_Nt =0A =0A =0A A =0A =0A =0A= =0A =0A 11 =0A =0A =0A H =0A =0A =0A HC =0A =0A =0A 0.0300000 = =0A =0A =0A =A00.060 =0A =0A =0A Ala_Nt =0A =0A =0A A =0A =0A =0A= =0A =0A 12 =0A =0A =0A H =0A =0A =0A HC =0A =0A =0A 0.0300000 = =0A =0A =0A =A00.060 =0A =0A =0A Ala_Nt =0A =0A =0A A =0A =0A =0A= =0A =0A 13 =0A =0A =0A N =0A =0A =0A N =0A =0A =0A -0.4157000 = =0A =0A =0A -0.416 =0A =0A =0A Ser =0A =0A =0A A =0A =0A =0A =0A = =0A 14 =0A =0A =0A H =0A =0A =0A H =0A =0A =0A 0.2719000 =0A = =0A =0A =A00.272 =0A =0A =0A Ser =0A =0A =0A A =0A =0A =0A =0A = =0A 15 =0A =0A =0A C =0A =0A =0A CT =0A =0A =0A -0.0249000 =0A = =0A =0A -0.025 =0A =0A =0A Ser =0A =0A =0A A =0A =0A =0A =0A =0A = 16 =0A =0A =0A H =0A =0A =0A H1 =0A =0A =0A 0.0843000 =0A =0A = =0A =A00.084 =0A =0A =0A Ser =0A =0A =0A A =0A =0A =0A =0A =0A 17= =0A =0A =0A C =0A =0A =0A C =0A =0A =0A 0.5973000 =0A =0A =0A = =A00.597 =0A =0A =0A Ser =0A =0A =0A A =0A =0A =0A =0A =0A 18 =0A = =0A =0A O =0A =0A =0A O =0A =0A =0A -0.5679000 =0A =0A =0A -0.5= 68 =0A =0A =0A Ser =0A =0A =0A A =0A =0A =0A =0A =0A 19 =0A =0A = =0A C =0A =0A =0A CT =0A =0A =0A 0.2117000 =0A =0A =0A =A00.212 = =0A =0A =0A Ser =0A =0A =0A A =0A =0A =0A =0A =0A 20 =0A =0A =0A= H =0A =0A =0A H1 =0A =0A =0A 0.0352000 =0A =0A =0A =A00.035 =0A = =0A =0A Ser =0A =0A =0A A =0A =0A =0A =0A =0A 21 =0A =0A =0A H = =0A =0A =0A H1 =0A =0A =0A 0.0352000 =0A =0A =0A =A00.035 =0A =0A= =0A Ser =0A =0A =0A A =0A =0A =0A =0A =0A 22 =0A =0A =0A O =0A = =0A =0A OH =0A =0A =0A -0.6546000 =0A =0A =0A -0.655 =0A =0A =0A= Ser =0A =0A =0A A =0A =0A =0A=0A=0A =A0This table includes the partial charges of first two residues (AlA & Ser= ) of protien. As seen, the partial charges of atoms of Ser in both cases ar= e the same but they are different in case these of ALA. My question how to know which program creating partial charges for ALA atom= s is right?? Best regards ***************************************************************************= ***********************Morad M. El-HendawyIRELAND ***************************************************************************= ***********************=A0If you want a happy life, do four things:=A01- Co= ntemplate and be thankful, 2- The past is gone forever, 3- Today all=0A that you have, 4- Leave the future alone until it come.=A0********************************= ***************************************************************************= ******** =0A=0A =0A=0A=0A --0-48102598-1258575302=:98383 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Morad
Regarding to your question, Par= tial Charges generated using GaussView are the correct ones, they are the s= ame exactly as in the AMBER implemented values (ALA N-terminus; called NALA= residue in AMBER).
About MOE, it has generated ALA charges considering = ALA as NON-terminus ALA residue (i.e. as ALA). This is where the difference= come from. May be this error returned to an error in defining your system = using MOE (your input file). Sorry, but I don't have much experience in usi= ng MOE to know why it happened.

P.S. my private email was dealing wi= th NON-Standard Residue.

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/a\compchem.net
Emai= l: m.ibrahim1982/a\yahoo.com
Website: www.compchem.net
Fax N= o.: +20862342601


--- On Wed, 11/18/09, = Morad El-Hendawy m80elhendawy]^[yahoo.com <owner-chemistry/a\ccl.net>= ; wrote:

From: Morad El-Hendawy m80elhend= awy]^[yahoo.com <owner-chemistry/a\ccl.net>
Subject: CCL:G: Partial = charges created by Gaussview
To: "Ibrahim, Mahmoud A. A. " <m= .ibrahim1982/a\yahoo.com>
Date: Wednesday, November 18, 2009, 5:49 PM
Hey every body,
I inquires about the relia= bilty of partial charges created by Gaussview in order to do MM calculation= using AMBER (Gaussian 09) for a certain protien. When I compared between t= he created partial charges of this protien using Gaussview and MOE (molecul= ar Operating Enviroment) using the same force field (AMBER94), I found the partial charge in both cases are the same except for the first residue ato= ms (ALA)  which is act as N-terminous as the following:

=0A=0A=0A =0A =0A =0A =0A =0A <= td style=3D"border-style: solid solid solid none; border-color: windowtext;= border-width: 1pt 1pt 1pt medium; padding: 0cm 5.4pt; width: 54pt;" valign= =3D"top" width=3D"72">=0A

MOE

=0A

Pa= rtial charges

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

5 =0A =0A

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

A

=0A =0A =0A =0A =0A =0A =0A =0A =0A =0A =0A =0A =0A =0A <= td style=3D"border-style: none solid solid none; border-color: windowtext; = border-width: medium 1pt 1pt medium; padding: 0cm 5.4pt; width: 46.15pt;" v= align=3D"top" width=3D"62">=0A

C

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

0.0300000

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

 0.597

=0A =0A =0A

Ser

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

0.2117000

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

H1

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

Ato= m No

=0A 		=0A

Atom symbol

=0A 		=0A

= AMBER type

=0A 		=0A

GaussView

=0A

Partial charges

=0A 		=0A

AMBER Fragment

=0A 		=0A

Chain

=0A
=0A

1

=0A =0A 		=0A

N

=0A = 		=0A

N3

=0A= 		=0A

0.1414000

=0A 		=0A

-0.416<= /span>

=0A 		=0A

Ala_Nt

=0A 		=0A

A

=0A
=0A

2

=0A =0A 		=0A

H

=0A =0A 		=0A

H

=0A <= /td>=0A 		=0A

0.1997000

=0A 		=0A

 0.272

=0A 		=0A

Ala_Nt

=0A 		=0A

A

=0A
=0A

3

=0A 		=0A

H

=0A 		=0A

H

=0A 		=0A

0.1997000

=0A = 		=0A

 0.272

=0A =0A 		=0A

Ala_Nt

=0A= 		=0A

A

= =0A
=0A

4

=0A 		=0A

H

=0A 		=0A

H

=0A 		=0A

0.1997000

=0A 		=0A

 0.272

=0A 		=0A

Ala_Nt

=0A 		=0A =

A

=0A
=0A

C<= /p> =0A

=0A

C= T

=0A 		=0A

0.0962000

=0A 		=0A

 0.034

=0A 		=0A

Ala_Nt

=0A
=0A

6

=0A 		= =0A

H

=0A 		=0A

HP

=0A 		=0A

0.0889000

=0A 		=0A

 0.082<= /p> =0A

=0A

A= la_Nt

=0A 		=0A

A

=0A
=0A <= p class=3D"MsoNormal" style=3D"text-align: justify;">7

=0A 		=0A

C

=0A 		=0A

0.6163000

=0A 		= =0A

=  0.597

=0A 		=0A=

Ala_Nt

=0A 		=0A

A

=0A
=0A

8

=0A 		=0A

O

=0A 		=0A

O

=0A 		=0A

-0.5722000

=0A 		=0A

-0.568

=0A 		= =0A

Ala_Nt

=0A 		=0A

A

=0A
=0A

9

=0A 		=0A

C

=0A 		=0A

CT

=0A 		=0A

-0.0597000

=0A = 		=0A

-0.183

=0A 		=0A

Ala_Nt

=0A 		=0A

A

=0A
=0A

10

=0A 		=0A

H

=0A 		=0A

HC

=0A 		=0A

0.0300000

=0A = 		=0A

 0.060

=0A =0A 		=0A

Ala_Nt

=0A= 		=0A

A

= =0A
=0A

11

=0A 		=0A

H

=0A 		=0A

HC

=0A 		=0A =

 = ;0.060

=0A 		=0A

Ala_Nt

=0A 		= =0A

A

=0A
=0A

12

=0A 		=0A

H

=0A 		=0A

HC

=0A 		=0A

0.0300000

=0A 		=0A

 0.060

=0A 		=0A

Ala_Nt

=0A 		=0A

A

=0A
=0A

13

=0A 		=0A

N

=0A 		=0A

N

=0A 		=0A

-0.415= 7000

=0A 		=0A

-0.416

=0A <= /td>=0A 		=0A

Ser

=0A= 		=0A

A

= =0A
=0A

14

=0A 		=0A

H

=0A 		=0A

H

=0A 		=0A

0.2719000

=0A 		= =0A

 0.272

=0A 		=0A

Ser

=0A 		=0A

A

=0A
=0A

15

=0A 		=0A

C

=0A 		=0A

CT

=0A 		=0A

-0.0249000 =0A

=0A

<= span style=3D"color: blue;">-0.025

=0A 		=0A

Ser

=0A 		=0A

A

=0A
=0A

16

=0A 		= =0A

H

=0A 		=0A

H1

=0A 		=0A

0.0843000<= /span>

=0A 		=0A

 0.084=

=0A 		=0A

Ser

=0A 		=0A

A

=0A
=0A

17

= =0A 		=0A

C =0A

=0A

C =0A

=0A

= 0.5973000

=0A 		=0A

A

=0A
=0A

18

=0A 		=0A

O

=0A 		=0A

O

=0A 		=0A

-0.567= 9000

=0A 		=0A

-0.568

=0A <= /td>=0A 		=0A

Ser

=0A= 		=0A

A

= =0A
=0A

19

=0A 		=0A

C

=0A 		=0A

CT

=0A 		=0A

 0.212

=0A 		=0A

Ser

=0A 		=0A

A

=0A
=0A

20

=0A 		=0A

H

=0A 		=0A

H1

=0A 		=0A

0.0352000 =0A

=0A

 0.035 =0A

=0A

Se= r

=0A 		=0A

A

=0A
=0A

21

=0A 		=0A

H

=0A 		=0A

0.0352000

=0A 		=0A

 0.035

=0A 		=0A

Ser

=0A 		=0A

A

=0A
=0A

22

=0A 		=0A

O

=0A 		=0A

OH

=0A 		=0A

-0.6546000 =0A

=0A

<= span style=3D"color: blue;">-0.655

=0A 		=0A

Ser

=0A 		=0A

A

=0A
=0A=0A
 This table includes the partial charges = of first two residues (AlA & Ser) of protien. As seen, the partial char= ges of atoms of Ser in both cases are the same but they are different in ca= se these of ALA.
My question how to know which program creating partial = charges for ALA atoms is right??
Best regards

*****************************= *********************************************************************
IRELAND=
***********************************************************= ***************************************
<= font style=3D"background-color: rgb(230, 230, 230);" color=3D"#00407f"> If you want a happy life, do four things:
 
1- Contemplate and be thankful,=
2- The past is go= ne forever,
3- Today all=0A that you have,
4- Leave the future alone = until it come. 
**************************************************************= *****************************************************
= 3D""

=0A=0A

=0A=0A=0A=0A --0-48102598-1258575302=:98383-- From owner-chemistry@ccl.net Wed Nov 18 16:20:01 2009 From: "Joe Corkery jcorkery=-=eyesopen.com" To: CCL Subject: CCL: fingerprints (or bitstrings) of compounds Message-Id: <-40707-091118160500-26147-FDAHXLtQDd1FvdKyLJQ18A- -server.ccl.net> X-Original-From: Joe Corkery Content-Language: en-US Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Wed, 18 Nov 2009 13:04:41 -0800 MIME-Version: 1.0 Sent to CCL by: Joe Corkery [jcorkery() eyesopen.com] Hi Demetrios, Fingerprints can easily be generated from SMILES strings using the LINGO me= thod available in OpenEye's new GraphSim toolkit (MACCS key and path-based = fingerprints are also available). All OpenEye products are free for non-com= mercial use. To request an academic license please go to the following loca= tion: http://www.eyesopen.com/forms/academic_license_app.php Regards, Joe Corkery -----Original Message----- > From: owner-chemistry+jcorkery=3D=3Deyesopen.com!A!ccl.net [mailto:owner-chem= istry+jcorkery=3D=3Deyesopen.com!A!ccl.net] On Behalf Of Demetrios Xenides xe= nides(~)uop.gr Sent: Wednesday, November 18, 2009 1:17 PM To: Joe Corkery Subject: CCL: fingerprints (or bitstrings) of compounds Sent to CCL by: "Demetrios Xenides" [xenides^-^uop.gr] Hi CCL community!!! I would greatly appreciate your kind assistance in the following: Is there any possible (preferably not commercial) way to convert smile name= s to bit strings? It would be also nice if you can point to some relevant (= online) data. Best Regards, Demetrios -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Wed Nov 18 16:56:00 2009 From: "Rajarshi Guha rajarshi.guha:+:gmail.com" To: CCL Subject: CCL: fingerprints (or bitstrings) of compounds Message-Id: <-40708-091118161446-2578-CtUua5fsnQ+ygFhnBWkBAg|*|server.ccl.net> X-Original-From: Rajarshi Guha Content-Type: multipart/alternative; boundary=0016e6d7eb460f643b0478aac06a Date: Wed, 18 Nov 2009 15:04:28 -0500 MIME-Version: 1.0 Sent to CCL by: Rajarshi Guha [rajarshi.guha()gmail.com] --0016e6d7eb460f643b0478aac06a Content-Type: text/plain; charset=ISO-8859-1 On Wed, Nov 18, 2009 at 1:17 PM, Demetrios Xenides xenides(~)uop.gr < owner-chemistry]![ccl.net> wrote: > > Sent to CCL by: "Demetrios Xenides" [xenides^-^uop.gr] > Hi CCL community!!! > > I would greatly appreciate your kind assistance in the following: > > Is there any possible (preferably not commercial) way to convert smile > names to bit strings? It would be also nice if you can point to some > relevant (online) data. > You can use the CDK to calculate a variety of fingerprints, by calling the library or by using an UI at http://rguha.net/code/java/cdkdesc.html -- Rajarshi Guha NIH Chemical Genomics Center --0016e6d7eb460f643b0478aac06a Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

On Wed, Nov 18, 2009 at 1:17 PM, Demetri= os Xenides xenides(~)uop.gr <owner-chemistry]![ccl.net= > wrote:

Sent to CCL by: "Demetrios =A0Xenides" [xenides^-^uop.gr]
Hi CCL community!!!

I would greatly appreciate your kind assistance in the following:

Is there any possible (preferably not commercial) way to convert smile name= s to bit strings? It would be also nice if you can point to some relevant (= online) data.

You can use the CDK to calculate a v= ariety of fingerprints, by calling the library or by using an UI at http://rguha.net/code/java/cdk= desc.html

--
Rajarshi Guha
NIH Chemical Genomics Center
--0016e6d7eb460f643b0478aac06a-- From owner-chemistry@ccl.net Wed Nov 18 17:33:01 2009 From: "=?utf-8?B?VEogTydEb25uZWxs?= tjo{}acm.org" To: CCL Subject: CCL: =?utf-8?B?UmU6IENDTDogZmluZ2VycHJpbnRzIChvciBiaXRzdHJpbmdzKSBvZiBjb21wb3VuZHM=?= Message-Id: <-40709-091118161450-2627-vSfTViHTDGzPM0xQU1lIRg^server.ccl.net> X-Original-From: "=?utf-8?B?VEogTydEb25uZWxs?=" Content-Type: multipart/alternative; boundary="----=_Part_0_1258575051521" Date: Wed, 18 Nov 2009 12:10:41 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: "=?utf-8?B?VEogTydEb25uZWxs?=" [tjo]-[acm.org] ------=_Part_0_1258575051521 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: base64 Content-Disposition: inline T3BlbkJhYmVsIGhhcyBhIGZpbmdlcnByaW50IGNhcGFiaWxpdHkKClRKIE8nRG9ubmVsbAoKLS0t LS0gUmVwbHkgbWVzc2FnZSAtLS0tLQpGcm9tOiAiRGVtZXRyaW9zIFhlbmlkZXMgeGVuaWRlcyh+ KXVvcC5nciIgPG93bmVyLWNoZW1pc3RyeUBjY2wubmV0PgpEYXRlOiBXZWQsIE5vdiAxOCwgMjAw OSAxMDoxNyBBTQpTdWJqZWN0OiBDQ0w6IGZpbmdlcnByaW50cyAob3IgYml0c3RyaW5ncykgb2Yg Y29tcG91bmRzClRvOiAiT0Rvbm5lbGwsIFQgSiAtaWQjM2FwLSIgPHRqb0Bnbm92YS5jb20+CgoK U2VudCB0byBDQ0wgYnk6ICJEZW1ldHJpb3MgIFhlbmlkZXMiIFt4ZW5pZGVzXi1edW9wLmdyXQpI aSBDQ0wgY29tbXVuaXR5ISEhCgpJIHdvdWxkIGdyZWF0bHkgYXBwcmVjaWF0ZSB5b3VyIGtpbmQg YXNzaXN0YW5jZSBpbiB0aGUgZm9sbG93aW5nOgoKSXMgdGhlcmUgYW55IHBvc3NpYmxlIChwcmVm ZXJhYmx5IG5vdCBjb21tZXJjaWFsKSB3YXkgdG8gY29udmVydCBzbWlsZSBuYW1lcyB0byBiaXQg c3RyaW5ncz8gSXQgd291bGQgYmUgYWxzbyBuaWNlIGlmIHlvdSBjYW4gcG9pbnQgdG8gc29tZSBy ZWxldmFudCAob25saW5lKSBkYXRhLgoKQmVzdCBSZWdhcmRzLApEZW1ldHJpb3MKCgoKLT0gVGhp cyBpcyBhdXRvbWF0aWNhbGx5IGFkZGVkIHRvIGVhY2ggbWVzc2FnZSBieSB0aGUgbWFpbGluZyBz Y3JpcHQgPS0KVG8gcmVjb3ZlciB0aGUgZW1haWwgYWRkcmVzcyBvZiB0aGUgYXV0aG9yIG9mIHRo ZSBtZXNzYWdlLCBwbGVhc2UgY2hhbmdlCnRoZSBzdHJhbmdlIGNoYXJhY3RlcnMgb24gdGhlIHRv cCBsaW5lIHRvIHRoZSBAIHNpZ24uIFlvdSBjYW4gYWxzbwpsb29rIHVwIHRoZSBYLU9yaWdpbmFs LUZyb206IGxpbmUgaW4gdGhlIG1haWwgaGVhZGVyLgoKRS1tYWlsIHRvIHN1YnNjcmliZXJzOiBD SEVNSVNUUllAY2NsLm5ldCBvciB1c2U6CiAgICAgIGh0dHA6Ly93d3cuY2NsLm5ldC9jZ2ktYmlu L2NjbC9zZW5kX2NjbF9tZXNzYWdlCgpFLW1haWwgdG8gYWRtaW5pc3RyYXRvcnM6IENIRU1JU1RS WS1SRVFVRVNUQGNjbC5uZXQgb3IgdXNlCiAgICAgIGh0dHA6Ly93d3cuY2NsLm5ldC9jZ2ktYmlu L2NjbC9zZW5kX2NjbF9tZXNzYWdlCgpTdWJzY3JpYmUvVW5zdWJzY3JpYmU6IAogICAgICBodHRw Oi8vd3d3LmNjbC5uZXQvY2hlbWlzdHJ5L3N1Yl91bnN1Yi5zaHRtbAoKQmVmb3JlIHBvc3Rpbmcs IGNoZWNrIHdhaXQgdGltZSBhdDogaHR0cDovL3d3dy5jY2wubmV0CgpKb2I6IGh0dHA6Ly93d3cu Y2NsLm5ldC9qb2JzIApDb25mZXJlbmNlczogaHR0cDovL3NlcnZlci5jY2wubmV0L2NoZW1pc3Ry eS9hbm5vdW5jZW1lbnRzL2NvbmZlcmVuY2VzLwoKU2VhcmNoIE1lc3NhZ2VzOiBodHRwOi8vd3d3 LmNjbC5uZXQvY2hlbWlzdHJ5L3NlYXJjaGNjbC9pbmRleC5zaHRtbAoKSWYgeW91ciBtYWlsIGJv dW5jZXMgZnJvbSBDQ0wgd2l0aCA1LjcuMSBlcnJvciwgY2hlY2s6CiAgICAgIGh0dHA6Ly93d3cu Y2NsLm5ldC9zcGFtbWVycy50eHQKClJURkk6IGh0dHA6Ly93d3cuY2NsLm5ldC9jaGVtaXN0cnkv YWJvdXRjY2wvaW5zdHJ1Y3Rpb25zLwoKCg== ------=_Part_0_1258575051521 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: base64 Content-Disposition: inline T3BlbkJhYmVsIGhhcyBhIGZpbmdlcnByaW50IGNhcGFiaWxpdHk8YnI+PGJyPlRKIE8mIzM5O0Rv bm5lbGw8YnI+PGJyPi0tLS0tIFJlcGx5IG1lc3NhZ2UgLS0tLS08YnI+RnJvbTogJnF1b3Q7RGVt ZXRyaW9zIFhlbmlkZXMgeGVuaWRlcyh+KXVvcC5nciZxdW90OyAmbHQ7b3duZXItY2hlbWlzdHJ5 QGNjbC5uZXQmZ3Q7PGJyPkRhdGU6IFdlZCwgTm92IDE4LCAyMDA5IDEwOjE3IEFNPGJyPlN1Ympl Y3Q6IENDTDogZmluZ2VycHJpbnRzIChvciBiaXRzdHJpbmdzKSBvZiBjb21wb3VuZHM8YnI+VG86 ICZxdW90O09Eb25uZWxsLCBUIEogLWlkIzNhcC0mcXVvdDsgJmx0O3Rqb0Bnbm92YS5jb20mZ3Q7 PGJyPjxicj48YnI+U2VudCB0byBDQ0wgYnk6ICZxdW90O0RlbWV0cmlvcyAmbmJzcDtYZW5pZGVz JnF1b3Q7IFt4ZW5pZGVzXi1edW9wLmdyXTxicj5IaSBDQ0wgY29tbXVuaXR5ISEhPGJyPjxicj5J IHdvdWxkIGdyZWF0bHkgYXBwcmVjaWF0ZSB5b3VyIGtpbmQgYXNzaXN0YW5jZSBpbiB0aGUgZm9s bG93aW5nOjxicj48YnI+SXMgdGhlcmUgYW55IHBvc3NpYmxlIChwcmVmZXJhYmx5IG5vdCBjb21t ZXJjaWFsKSB3YXkgdG8gY29udmVydCBzbWlsZSBuYW1lcyB0byBiaXQgc3RyaW5ncz8gSXQgd291 bGQgYmUgYWxzbyBuaWNlIGlmIHlvdSBjYW4gcG9pbnQgdG8gc29tZSByZWxldmFudCAob25saW5l KSBkYXRhLjxicj48YnI+QmVzdCBSZWdhcmRzLDxicj5EZW1ldHJpb3M8YnI+PGJyPjxicj48YnI+ LT0gVGhpcyBpcyBhdXRvbWF0aWNhbGx5IGFkZGVkIHRvIGVhY2ggbWVzc2FnZSBieSB0aGUgbWFp bGluZyBzY3JpcHQgPS08YnI+VG8gcmVjb3ZlciB0aGUgZW1haWwgYWRkcmVzcyBvZiB0aGUgYXV0 aG9yIG9mIHRoZSBtZXNzYWdlLCBwbGVhc2UgY2hhbmdlPGJyPnRoZSBzdHJhbmdlIGNoYXJhY3Rl cnMgb24gdGhlIHRvcCBsaW5lIHRvIHRoZSBAIHNpZ24uIFlvdSBjYW4gYWxzbzxicj5sb29rIHVw IHRoZSBYLU9yaWdpbmFsLUZyb206IGxpbmUgaW4gdGhlIG1haWwgaGVhZGVyLjxicj48YnI+RS1t YWlsIHRvIHN1YnNjcmliZXJzOiBDSEVNSVNUUllAY2NsLm5ldCBvciB1c2U6PGJyPiAmbmJzcDsg Jm5ic3A7ICZuYnNwOzxhIGhyZWY9Imh0dHA6Ly93d3cuY2NsLm5ldC9jZ2ktYmluL2NjbC9zZW5k X2NjbF9tZXNzYWdlIj5odHRwOi8vd3d3LmNjbC5uZXQvY2dpLWJpbi9jY2wvc2VuZF9jY2xfbWVz c2FnZTwvYT48YnI+PGJyPkUtbWFpbCB0byBhZG1pbmlzdHJhdG9yczogQ0hFTUlTVFJZLVJFUVVF U1RAY2NsLm5ldCBvciB1c2U8YnI+ICZuYnNwOyAmbmJzcDsgJm5ic3A7PGEgaHJlZj0iaHR0cDov L3d3dy5jY2wubmV0L2NnaS1iaW4vY2NsL3NlbmRfY2NsX21lc3NhZ2UiPmh0dHA6Ly93d3cuY2Ns Lm5ldC9jZ2ktYmluL2NjbC9zZW5kX2NjbF9tZXNzYWdlPC9hPjxicj48YnI+U3Vic2NyaWJlL1Vu c3Vic2NyaWJlOiA8YnI+ICZuYnNwOyAmbmJzcDsgJm5ic3A7PGEgaHJlZj0iaHR0cDovL3d3dy5j Y2wubmV0L2NoZW1pc3RyeS9zdWJfdW5zdWIuc2h0bWwiPmh0dHA6Ly93d3cuY2NsLm5ldC9jaGVt aXN0cnkvc3ViX3Vuc3ViLnNodG1sPC9hPjxicj48YnI+QmVmb3JlIHBvc3RpbmcsIGNoZWNrIHdh aXQgdGltZSBhdDogPGEgaHJlZj0iaHR0cDovL3d3dy5jY2wubmV0Ij5odHRwOi8vd3d3LmNjbC5u ZXQ8L2E+PGJyPjxicj5Kb2I6IDxhIGhyZWY9Imh0dHA6Ly93d3cuY2NsLm5ldC9qb2JzIj5odHRw Oi8vd3d3LmNjbC5uZXQvam9iczwvYT4gPGJyPkNvbmZlcmVuY2VzOiA8YSBocmVmPSJodHRwOi8v c2VydmVyLmNjbC5uZXQvY2hlbWlzdHJ5L2Fubm91bmNlbWVudHMvY29uZmVyZW5jZXMvPGJyIj5o dHRwOi8vc2VydmVyLmNjbC5uZXQvY2hlbWlzdHJ5L2Fubm91bmNlbWVudHMvY29uZmVyZW5jZXMv PGJyPC9hPj48YnI+U2VhcmNoIE1lc3NhZ2VzOiA8YSBocmVmPSJodHRwOi8vd3d3LmNjbC5uZXQv Y2hlbWlzdHJ5L3NlYXJjaGNjbC9pbmRleC5zaHRtbCI+aHR0cDovL3d3dy5jY2wubmV0L2NoZW1p c3RyeS9zZWFyY2hjY2wvaW5kZXguc2h0bWw8L2E+PGJyPjxicj5JZiB5b3VyIG1haWwgYm91bmNl cyBmcm9tIENDTCB3aXRoIDUuNy4xIGVycm9yLCBjaGVjazo8YnI+ICZuYnNwOyAmbmJzcDsgJm5i c3A7PGEgaHJlZj0iaHR0cDovL3d3dy5jY2wubmV0L3NwYW1tZXJzLnR4dCI+aHR0cDovL3d3dy5j Y2wubmV0L3NwYW1tZXJzLnR4dDwvYT48YnI+PGJyPlJURkk6IDxhIGhyZWY9Imh0dHA6Ly93d3cu Y2NsLm5ldC9jaGVtaXN0cnkvYWJvdXRjY2wvaW5zdHJ1Y3Rpb25zLzxiciI+aHR0cDovL3d3dy5j Y2wubmV0L2NoZW1pc3RyeS9hYm91dGNjbC9pbnN0cnVjdGlvbnMvPGJyPC9hPj48YnI+PGJyPjxi cj48YnI+ ------=_Part_0_1258575051521-- From owner-chemistry@ccl.net Wed Nov 18 18:06:01 2009 From: "Joe Leonard jleonard42-$-gmail.com" To: CCL Subject: CCL: PLS implementation? Message-Id: <-40710-091118180143-9398-9/BO6zVaZTSJV6IXPsFC1g{:}server.ccl.net> X-Original-From: Joe Leonard Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Date: Wed, 18 Nov 2009 18:01:15 -0500 Mime-Version: 1.0 (Apple Message framework v936) Sent to CCL by: Joe Leonard [jleonard42|gmail.com] Folks, I would appreciate any pointers to PLS implementations that can handle much larger number of X variables as compared to Y (to-be-fit) variables. I recall that PLS was used in 3D QSAR applications because of its stability in such cases, but it seems that individual implementations differ in how this statement applies to them... 3D QSAR test sets w/ aligned compounds would also be of use - if people are aware of such collections on-line. But the PLS engine(s) are my primary search right now... Thanks in advance! Joe Leonard jleonard42.:.gmail.com -- I have fought a good fight, I have finished my course, I have kept the faith. EFL/11-6-09 From owner-chemistry@ccl.net Wed Nov 18 20:14:01 2009 From: "Jeff Woodford jwoodfor]=[eou.edu" To: CCL Subject: CCL:G: G IRC run goes in same direction Message-Id: <-40711-091118172731-30528-bc2gnNhguOl/f2xFqn4yQw~~server.ccl.net> X-Original-From: "Jeff Woodford" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 18 Nov 2009 13:57:22 -0800 MIME-Version: 1.0 Sent to CCL by: "Jeff Woodford" [jwoodfor:_:eou.edu] My guess is that you aren't at a true transition state. Is the imaginary frequency very small in magnitude? This same thing has happened to me when I don't use tight convergence criterion for calculating the hessian, resulting in numerical error for the rotational/translational modes and a spurious "imaginary" frequency. When I tighten the convergence criterion, the imaginary frequency goes away. Just a guess. -Jeff Jeffrey N. Woodford Associate Professor of Chemistry Eastern Oregon University Tel: 541-962-3321 Fax: 541-962-3873 -----Original Message----- > From: owner-chemistry+jwoodfor==eou.edu-.-ccl.net [mailto:owner-chemistry+jwoodfor==eou.edu-.-ccl.net] On Behalf Of Peter M Burger burger~~chemie.uni-hamburg.de Sent: Wednesday, November 18, 2009 10:06 AM To: Woodford, Jeffrey N Subject: CCL:G: G IRC run goes in same direction Sent to CCL by: "Peter M Burger" [burger**chemie.uni-hamburg.de] Hello, I noticed that the following question was asked before here but did not find a conclusive answer. So what can be done if an IRC run in g03 goes in the same direction for both the reverse and forward keywords? Regards Peterhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Wed Nov 18 21:36:00 2009 From: "Roby Kurian Roby_Kurian^^umit.maine.edu" To: CCL Subject: CCL: ONIOM optimization of Gold compound Message-Id: <-40712-091118113451-3504-B4jnB1a3r92AZNFFflyiRw*o*server.ccl.net> X-Original-From: "Roby Kurian" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 18 Nov 2009 10:53:50 -0500 MIME-Version: 1.0 Sent to CCL by: "Roby Kurian" [Roby_Kurian===umit.maine.edu] Hi, I was trying to optimize a Gold compound (Gold bonded to glutathione) using ONIOM. There are two levels of theory being used, B3LYP/6-31+g(d) for higher layer and UFF for lower layer. I have defined Gold atom using LANL2DZ-ECP. Now the calculation has converged but all atoms (including those were in lower mechanics layer) ended up in upper(quantum) layer. The input I gave was # opt=modredundant oniom (b3lyp)/genecp geom=connectivity (Name) (Molecular defenition in Z-matrix) C H O N S P Cl 6-31+g(d):uff **** (LANL2DZ ECP from EMSL Basis Set Exchange Library) So any suggestions for modifying the route so that all atoms stay in the defined lavel? Thanks and Regards Roby Kurian Dept. of Chemistry University of Maine