For more information and to download a demo version visit:

--0016e6d26cf192e7400478b32154-- From owner-chemistry@ccl.net Thu Nov 19 06:37:01 2009 From: "Mahmoud A. A. Ibrahim m.ibrahim1982/./yahoo.com" To: CCL Subject: CCL: ONIOM optimization of Gold compound Message-Id: <-40714-091119063603-9939-o8CW68VLV4InJgBD5nYXWg-,-server.ccl.net> X-Original-From: "Mahmoud A. A. Ibrahim" Content-Type: multipart/alternative; boundary="0-333936961-1258630548=:62486" Date: Thu, 19 Nov 2009 03:35:48 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim1982.[A].yahoo.com] --0-333936961-1258630548=:62486 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Roby According to your Route Section, you have asked for one layer calculation u= sing b3lyp/genecp. The problem is returned to defining the keywords and bas= is set. You have to change your route section to: # opt=3Dmodredundant oniom (b3lyp/genecp:uff) geom=3Dconnectivity Card Title Charge and Multiplicity (Molecular defenition in Z-matrix) ...... ... .. . C H O N S P Cl 0 LANL2DZ **** C H O N S P Cl 0 LANL2DZ ----------------------------------- Sorry, but you said you have Gold in your system, I couldn't see it when yo= u defined the ECP basis set. I have another comment, why do you use UFF force field? think twice before = using it. Check your system again. 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, Roby Kurian Roby_Kurian^^umit.maine.edu wrote: > From: Roby Kurian Roby_Kurian^^umit.maine.edu Subject: CCL: ONIOM optimization of Gold compound To: "Ibrahim, Mahmoud A. A. " Date: Wednesday, November 18, 2009, 3:53 PM Sent to CCL by: "Roby Kurian" [Roby_Kurian=3D=3D=3Dumit.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 high= er layer and UFF for lower layer. I have defined Gold atom using LANL2DZ-EC= P. Now the calculation has converged but all atoms (including those were in lo= wer mechanics layer) ended up in upper(quantum) layer. The input I gave was # opt=3Dmodredundant oniom (b3lyp)/genecp geom=3Dconnectivity (Name) (Molecular defenition in Z-matrix) C H O N S P Cl 6-31+g(d):uff **** (LANL2DZ ECP from EMSL=A0 Basis Set Exchange Library) So any suggestions for modifying the route so that all atoms stay in the de= fined lavel? Thanks and Regards Roby Kurian Dept. of Chemistry University of Maine -=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 --0-333936961-1258630548=:62486 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable

Dear Roby
According to your Route Section,= you have asked for one layer calculation using b3lyp/genecp. The problem i= s returned to defining the keywords and basis set.
You have to change yo= ur route section to:

# opt=3Dmodredundant oniom (b3lyp/genecp:uff) g= eom=3Dconnectivity

Card Title

Charge and Multiplicity
(Mol= ecular defenition in Z-matrix)
......
...
..
.

C H O N S= P Cl 0
LANL2DZ
****

C H O N S P Cl 0
LANL2DZ

--= ---------------------------------

Sorry, but you said you have Gold = in your system, I couldn't see it when you defined the ECP basis set.
I = have another comment, why do you use UFF force field? think twice before us= ing it.
Check your system again.
Sincerely;
M. Ibrahim

=

Mahmoud A. A. Ibrahim

Current Add= ress

= 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[A]= compchem.net
Email: m.ibrahim1982[A]yahoo.com
Website: www.compchem.net=
Fax No.: +20862342601

--- O= n Wed, 11/18/09, Roby Kurian Roby_Kurian^^umit.maine.edu <owner-chemistry[A]c= cl.net> wrote:

From: Roby Kurian= Roby_Kurian^^umit.maine.edu <owner-chemistry[A]ccl.net>
Subject: CC= L: ONIOM optimization of Gold compound
To: "Ibrahim, Mahmoud A. A. -id#4= 2s-" <m.ibrahim1982[A]yahoo.com>
Date: Wednesday, November 18, 2009,= 3:53 PM

Sent to CCL by: "Roby Kurian" = [Roby_Kurian=3D=3D=3Dumit.maine.edu]
Hi,

I was trying to optimize= a Gold compound (Gold bonded to glutathione) using ONIOM. There are two le= vels of theory being used, B3LYP/6-31+g(d) for higher layer and UFF for low= er layer. I have defined Gold atom using LANL2DZ-ECP.

Now the calcul= ation has converged but all atoms (including those were in lower mechanics = layer) ended up in upper(quantum) layer.

The input I gave was
# opt=3Dmodredundant oniom (b3lyp)/genecp geom=3Dconnectivity

(Name)<= br>(Molecular defenition in Z-matrix)

C H O N S P Cl
6-31+g(d= ):uff
****

(LANL2DZ ECP from EMSL Basis Set Exchange Librar= y)

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

-=3D This is autom= atically added to each message by the mailing script =3D-
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=0A= =0A=0A=0A --0-333936961-1258630548=:62486-- From owner-chemistry@ccl.net Thu Nov 19 07:53:01 2009 From: "Jean-Christophe Poully poully%galilee.univ-paris13.fr" To: CCL Subject: CCL:G: ONIOM optimization of Gold compound Message-Id: <-40715-091119065416-18278-9PZycwjsC6/SVpmAn/4uhA!^!server.ccl.net> X-Original-From: Jean-Christophe Poully Content-Type: text/plain; charset="us-ascii"; format=flowed Date: Thu, 19 Nov 2009 12:14:35 +0100 Mime-Version: 1.0 Sent to CCL by: Jean-Christophe Poully [poully**galilee.univ-paris13.fr] Dear Roby, You have to define your geometry by using cartesian coordinates, and not Z-matrix. For each atom you have to tell Gaussian (if you use this program) which layer it belongs to (H or L), and precise that you use uff as low layer in the # line. Check out the Gaussian user manual for more information. Hope this helps, Jean-Christophe Poully At 16:53 18/11/2009, you wrote: >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 From owner-chemistry@ccl.net Thu Nov 19 08:42:01 2009 From: "Justin Finnerty justin.finnerty-*-uni-oldenburg.de" To: CCL Subject: CCL:G: G IRC run goes in same direction Message-Id: <-40716-091119082211-28169-er1nFeQgxQ3KBxsq40Lppg|*|server.ccl.net> X-Original-From: Justin Finnerty Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8 Date: Thu, 19 Nov 2009 14:21:53 +0100 Mime-Version: 1.0 Sent to CCL by: Justin Finnerty [justin.finnerty-,-uni-oldenburg.de] Hello Peter, I find that this is a common situation with B3LYP and some other DFT methods. I find this situtation even when the correct transition state with large magnitude is found and scf=tight convergence. In this situation my solution is to use a small step-size and to "nudge" the structure in the direction it is not going. I do the "nudge" by looking at the difference between the initial and first geometry of the IRC from the first direction. I then modify the original structure by half this movement in the opposite direction. Cheers Justin On Wed, 2009-11-18 at 13:06 -0500, Peter M Burger burger~~chemie.uni-hamburg.de wrote: > 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 > -- Dr Justin Finnerty Rm W3-1-165 Ph 49 (441) 798 3726 Carl von Ossietzky Universität Oldenburg From owner-chemistry@ccl.net Thu Nov 19 09:19:00 2009 From: "davide ricci ricci#hbarsol.com" To: CCL Subject: CCL: Computer-aided chemistry has never been so easy!! Message-Id: <-40717-091119075659-15763-PiUtB0nmu9GwcB6mPcZufw[]server.ccl.net> X-Original-From: "davide ricci" Date: Thu, 19 Nov 2009 07:56:55 -0500 Sent to CCL by: "davide ricci" [ricci:-:hbarsol.com] hBar Solutions ApS is proud to announce that hBar Lab beta is now available! hBar Lab beta is the first web application for the simulation of properties of molecules, like EA, IP. There is no need of expert knowledge and there is no hassle with software and hardware. There is no need for expensive licenses and you only pay for what you use! Discover what hBar Lab beta can do for you at www.hbar-lab.com From owner-chemistry@ccl.net Thu Nov 19 09:52:01 2009 From: "ga mi ou oumigapi###yahoo.cn" To: CCL Subject: CCL:G: how to perform Natural Transition Orbial with Gaussian09 Message-Id: <-40718-091119015804-14214-i39Kd5k4sDCNONcpxKeGKg###server.ccl.net> X-Original-From: "ga mi ou" Date: Thu, 19 Nov 2009 01:58:00 -0500 Sent to CCL by: "ga mi ou" [oumigapi:yahoo.cn] Hello, everyone, I try to perform natural transition orbital(NTO) analysis with Gaussian09 according to G09 manual, but always failed. Here is my route section inptut: # opt td=(root=1,nstates=6) b3lyp/6-31g(d) density=transition=1 pop(NTO,saveNTO) Can anyone kindly tell me how to get NTOs with G09? If it is possible, can you please send me a input sample? Thank you very much, Best Regards, miga From owner-chemistry@ccl.net Thu Nov 19 10:27:01 2009 From: "Markus Kossner m.kossner.(~).tu-bs.de" To: CCL Subject: CCL: fingerprints (or bitstrings) of compounds Message-Id: <-40719-091118191546-23210-sJYDay9mv51tSsD60s6f3Q(~)server.ccl.net> X-Original-From: Markus Kossner Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Thu, 19 Nov 2009 00:43:04 +0100 MIME-Version: 1.0 Sent to CCL by: Markus Kossner [m.kossner^_^tu-bs.de] Have a look at the RDKit: www.rdkit.org Cheers Markus Quoting "Demetrios Xenides xenides(~)uop.gr" : > > 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 =20 > smile names to bit strings? It would be also nice if you can point =20 > to some relevant (online) data. > > Best Regards, > Demetrios > > > > -=3D This is automatically added to each message by the mailing script =3D= -> > > From owner-chemistry@ccl.net Thu Nov 19 11:02:00 2009 From: "John McKelvey jmmckel*o*gmail.com" To: CCL Subject: CCL: Computing volumes in G03 Message-Id: <-40720-091119093201-12603-XFmqvb1kHyxRkJjJwGaucQ() server.ccl.net> X-Original-From: John McKelvey Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 19 Nov 2009 09:31:45 -0500 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel]^[gmail.com] Folks, I have been computing volumes using CISD/6-311G* SCF=TIGHT VOLUME=TIGHT for first and second row atoms with charges of +1, 0, and -1 (and of course the appropriate multiplicities.) I find differences between replicate runs to be as large as 20 percent. I know that the answers are supposed to be approximate, but is there any way to tighten this up, perhaps by putting more points "in the box", or any other means? Many thanks! John -- John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel^_^gmail.com From owner-chemistry@ccl.net Thu Nov 19 11:37:01 2009 From: "John McKelvey jmmckel,,gmail.com" To: CCL Subject: CCL: Slight error in previous post.. Message-Id: <-40721-091119112304-11435-cqZwfoLzXGZ0Q01TJPbBNA.:.server.ccl.net> X-Original-From: John McKelvey Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 19 Nov 2009 11:22:53 -0500 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel,gmail.com] Aplolgies.. Should have said 6-311+G*.. John -- John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel---gmail.com From owner-chemistry@ccl.net Thu Nov 19 12:13:00 2009 From: "Morad El-Hendawy m80elhendawy~!~yahoo.com" To: CCL Subject: CCL:G: Gaussian 03 + Exceeded Z-Matrix Message-Id: <-40722-091119112428-13150-ZybRhjhzkf1PcfbBeBGiIw[]server.ccl.net> X-Original-From: Morad El-Hendawy Content-Type: multipart/alternative; boundary="0-981291223-1258647857=:19018" Date: Thu, 19 Nov 2009 08:24:17 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Morad El-Hendawy [m80elhendawy()yahoo.com] --0-981291223-1258647857=:19018 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hey every body, I got the following error when I submit an input file for protien of about = 27000 atoms in order to do AMBER94 calculation using Gaussian 03: "The maximum of 20000 Z-matrix cards has been exceeded Error termination via Lnk1e in C:\G03W\l101.exe" I guess that this error due to exceeding Z-matrix more than 20000 atoms. Is= there a keyword=A0 to solve this problem. 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 --0-981291223-1258647857=:19018 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable

Hey every body,
I got the following error = when I submit an input file for protien of about 27000 atoms in order to do= AMBER94 calculation using Gaussian 03:

"The maximum of 20000 Z-matrix cards ha= s been exceeded
Er= ror termination via Lnk1e in C:\G03W\l101.exe"

I guess that this error due to = exceeding Z-matrix more than 20000 atoms. Is there a keyword to solve= this problem.
Best regards,
**************************************************************= ************************************

Morad M. El-Hendawy

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

<= strong>

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.

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

=0A=0A=0A=0A --0-981291223-1258647857=:19018-- From owner-chemistry@ccl.net Thu Nov 19 13:39:01 2009 From: "Jan Labanowski janl-$-speakeasy.net" To: CCL Subject: CCL: Chemical Computing Group Inc. Releases GOLD Integration Technology Message-Id: <-40723-091119133435-1324-nZPh83krMJWY1PEv6XWyNQ+/-server.ccl.net> X-Original-From: Jan Labanowski Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 19 Nov 2009 13:34:22 EST MIME-Version: 1.0 Sent to CCL by: Jan Labanowski [janl]*[speakeasy.net] MONTREAL, November 19, 2009 =E2=80=93 Chemical Computing Group Inc. (CCG) a= nnounces the general release of a graphical interface for Cambridge Crystallographic Data Centre=E2=80=99s (CCDC=E2=80=99s) GOLD docking software as part of CCG=E2= =80=99s Molecular Operating Environment (MOE) software package. The integration technology will be avai= lable in the 2009.10 version of MOE. While the two software programs must be licensed separately, the new interf= ace will make running the GOLD docking program from within the MOE software sea= mless for end-users. The interface also allows end-users to conveniently modify = GOLD parameters during the simulation. Paul Labute, President and CEO of CCG said that =E2=80=9CGOLD is an industr= y leading protein-ligand docking engine and CCG has worked over the past year to comb= ine the strengths of MOE and GOLD. MOE contains leading preparation and post-processing functionality while GOLD specifically addresses the docking problem. The combination will be of great benefit to CCG and CCDC customers since MOE=E2=80=99s proton placement, pharmacophore screening, and structur= e refinement technology can be combined with GOLD directly.=E2=80=9D Labute went on to say that =E2=80=9CMany of our customers use MOE as a cent= ral platform for their computational pharmaceuticals research and, in recent years, CCG = has added components to combine MOE=E2=80=99s strengths with third-party applic= ations. We are very pleased to include GOLD in this capacity and initial customer reac= tion to the MOE-GOLD link has been very positive.=E2=80=9D Chemical Computing Group Inc. (www.chemcomp.com) is a leading supplier of software solutions for Life Sciences. CCG=E2=80=99s drug discovery softwar= e platform is the Molecular Operating Environment (MOE) that integrates visualization, simulations and methodology development in one package. CCG=E2=80=99s info= rmatics platform is PSILO which is used for macromolecular structure registration, version control and web-based searching. CCG's products and services are u= sed by biologists, medicinal chemists and computational chemists in pharmaceutical/biotechnology companies, government organizations and univer= sities throughout the world. CCG is headquartered in Montreal, Canada. Email inquiries can be sent to info : chemcomp.com. ------- Posted by CCL admin, Jan Labanowski, since it is not longer than 25 lines (= at least on my terminal). From owner-chemistry@ccl.net Thu Nov 19 14:15:01 2009 From: "Andreas Uhe Uhe(a)itmc.rwth-aachen.de" To: CCL Subject: CCL:G: G IRC run goes in same direction Message-Id: <-40724-091119063905-10845-bzQCqE8FTruU3rS6kyKiyQ[a]server.ccl.net> X-Original-From: Andreas Uhe Content-type: multipart/alternative; boundary="Boundary_(ID_yWoCHc4A1oY4fV24tvjO+Q)" Date: Thu, 19 Nov 2009 12:08:46 +0100 MIME-version: 1.0 Sent to CCL by: Andreas Uhe [Uhe]_[itmc.rwth-aachen.de] This is a multi-part message in MIME format. --Boundary_(ID_yWoCHc4A1oY4fV24tvjO+Q) Content-type: text/plain; charset=ISO-8859-15; format=flowed Content-transfer-encoding: 8BIT Hello Peter, I encountered a similar problem a couple of times. For me it helped to specify a phase: IRC=(...,phase=(...,...),...) From the Gaussian Manual regarding the IRC keyword *Phase*=(/N1 N2/ [/N3/ [/N4/]]) Defines the phase for the transition vector such that "forward" motion along the transition vector corresponds to an increase in the specified internal coordinate, designated by up to four atom numbers. If two atom numbers are given, the coordinate is a bond stretch between the two atoms; three atom numbers specify an angle bend, and four atoms define a dihedral angle. Good luck, Andi Am 18.11.2009 19:06, schrieb Peter M Burger burger~~chemie.uni-hamburg.de: > 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> > > -- Dipl. Chem. Andreas Uhe RWTH Aachen Institut f�r Technische und Makromolekulare Chemie (ITMC) Worringer Weg 1 52074 Aachen E-mail: Uhe() itmc.rwth-aachen.de Tel.: 0049 - 241 - 80-26453 --Boundary_(ID_yWoCHc4A1oY4fV24tvjO+Q) Content-type: text/html; charset=ISO-8859-15 Content-transfer-encoding: 8BIT Hello Peter,

I encountered a similar problem a couple of times. For me it helped to specify a phase: IRC=(...,phase=(...,...),...)

> From the Gaussian Manual regarding the IRC keyword
Phase=(N1 N2 [N3 [N4]])
Defines the phase for the transition vector such that "forward" motion along the transition vector corresponds to an increase in the specified internal coordinate, designated by up to four atom numbers. If two atom numbers are given, the coordinate is a bond stretch between the two atoms; three atom numbers specify an angle bend, and four atoms define a dihedral angle.

Good luck,
Andi

Am 18.11.2009 19:06, schrieb Peter M Burger burger~~chemie.uni-hamburg.de:

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 

PeterE-mail to subscribers: CHEMISTRY() ccl.net or use:
      http://www.ccl.net/cgi-bin/ccl/send_ccl_message

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      http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtml

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-- 
Dipl. Chem. Andreas Uhe

RWTH Aachen
Institut f�r Technische und Makromolekulare Chemie (ITMC)
Worringer Weg 1
52074 Aachen
E-mail: Uhe() itmc.rwth-aachen.de
Tel.: 0049 - 241 - 80-26453

--Boundary_(ID_yWoCHc4A1oY4fV24tvjO+Q)-- From owner-chemistry@ccl.net Thu Nov 19 14:49:00 2009 From: "John McKelvey jmmckel ~ gmail.com" To: CCL Subject: CCL: Accurate Volomes Message-Id: <-40725-091119140544-30396-QEOs90hWdjt8G9H28b8s0w/a\server.ccl.net> X-Original-From: John McKelvey Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 19 Nov 2009 14:05:31 -0500 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel(a)gmail.com] Folks, I found the answer.. If one has ever tried computing pi to .01 accuracy using a random number generator and the circle inscribed in a square method, one immediately requires a Huge! number of points.. For volume accuracy for Carbon using 6-311+G* it was necessary to raise the number of points in boihrs**3 from the default value of 20 to a value of 40,000... Cheers! John -- John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel ~~ gmail.com From owner-chemistry@ccl.net Thu Nov 19 15:39:00 2009 From: "Dr David N Haney haney_+_edusoft-lc.com" To: CCL Subject: CCL: PLS implementation? Message-Id: <-40726-091119024209-3049-0WRY0lQvkMY5jmZdPxXtwA:+:server.ccl.net> X-Original-From: Dr David N Haney Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Wed, 18 Nov 2009 22:29:11 -0800 Mime-Version: 1.0 Sent to CCL by: Dr David N Haney [haney^^edusoft-lc.com] Joe, I dont know what type of software you are looking for. Certainly MATLAB has a PLS TOOLKIT. Or if you are looking for some older UNIX freeware, Mike Denham of University of Reading has some software. Goto: http://www.biostat.wustl.edu/archives/html/s-news/1999-06/msg00048.html On Wed, Nov 18, 2009 at 06:01:15PM -0500, Joe Leonard jleonard42-$-gmail.com wrote: > > 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> -- ######### David N. Haney, Ph.D. ######### # EduSoft, LC Phone - 858-483-1197 # # 5455 Westknoll Dr. FAX - 858-483-1046 # # La Jolla, CA 92037 Email - haney%%edusoft-lc.com # ################# ##################### From owner-chemistry@ccl.net Thu Nov 19 17:45:01 2009 From: "luisfer*edu.xunta.es" To: CCL Subject: CCL:G: G IRC run goes in same direction Message-Id: <-40727-091119154235-7907-Umg5wU1zJc42GSdLUaLaFw{}server.ccl.net> X-Original-From: Content-Disposition: inline Content-Language: gl Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=iso-8859-1 Date: Thu, 19 Nov 2009 19:30:22 +0100 MIME-Version: 1.0 Sent to CCL by: [luisfer|-|edu.xunta.es] Dear Jeff=2E Are you sure that the optimized Transition Structure that you use for IR= C calculations has one and only one negative vibration frequency=3F=2E Best regards=2E =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D Luis F=2E R=2E V=E1zquez Obradoiro de Qu=EDmica Te=F3rica e Computacional Real Sociedad Espa=F1ola de Qu=EDmica=2E Grupo de F=EDsica At=F3mica y M= olecular Sociedade Portuguesa de Qu=EDmica=2E Divi=E7ao de Qu=EDmica F=EDsica R=FAa Tornos=2C 21=2C piso 3 15007 A Coru=F1a Tel=2E +34 676 300 472 Correo-e luisfer=40edu=2Exunta=2Ees =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D ----- Mensaxe orixinal ----- De=3A =22Jeff Woodford jwoodfor=5D=3D=5Beou=2Eedu=22 =3Cowner-chemistry=40= ccl=2Enet=3E Data=3A M=E9rcores=2C Novembro 18=2C 2009 10=3A57 pm Asunto=3A CCL=3AG=3A G IRC run goes in same direction =3E = =3E Sent to CCL by=3A =22Jeff Woodford=22 =5Bjwoodfor=3A=5F=3Aeou=2Eedu=5D= =3E My guess is that you aren=27t at a true transition state=2E Is the = =3E imaginaryfrequency very small in magnitude=3F This same thing has = =3E happened to me when =3E I don=27t use tight convergence criterion for calculating the hessia= n=2C =3E resulting in numerical error for the rotational/translational modes = =3E and a =3E spurious =22imaginary=22 frequency=2E When I tighten the convergenc= e = =3E criterion=2Cthe imaginary frequency goes away=2E =3E = =3E Just a guess=2E =3E = =3E -Jeff =3E = =3E Jeffrey N=2E Woodford =3E Associate Professor of Chemistry =3E Eastern Oregon University =3E Tel=3A 541-962-3321 =3E Fax=3A 541-962-3873 =3E = =3E -----Original Message----- =3E =3E From=3A owner-chemistry+jwoodfor=3D=3Deou=2Eedu=5D=5F=5Bccl=2Ene= t =3E =5Bmailto=3Aowner-chemistry+jwoodfor=3D=3Deou=2Eedu=5D=5F=5Bccl=2Ene= t=5D On Behalf Of = =3E Peter M =3E Burger burger=7E=7Echemie=2Euni-hamburg=2Ede =3E Sent=3A Wednesday=2C November 18=2C 2009 10=3A06 AM =3E To=3A Woodford=2C Jeffrey N = =3E Subject=3A CCL=3AG=3A G IRC run goes in same direction =3E = =3E = =3E Sent to CCL by=3A =22Peter M Burger=22 =5Bburger**chemie=2Euni-hambu= rg=2Ede=5D =3E Hello=2C =3E = =3E I noticed that the following question was asked before here but did = =3E not find =3E a = =3E conclusive answer=2E =3E = =3E So what can be done if an IRC run in g03 goes in the same direction = =3E for both =3E = =3E the reverse and forward keywords=3F =3E = =3E Regards = =3E = =3E Peterhttp=3A//www=2Eccl=2Enet/cgi- =3E bin/ccl/send=5Fccl=5Fmessagehttp=3A//www=2Eccl=2Enet/chemistry/sub=5F= unsub=2Eshtmlhttp=3A//www=2Eccl=2Enet/spammers=2Etxt =3E = =3E -=3D This is automatically added to each message by the mailing = =3E script =3D- =3E To recover the email address of the author of the message=2C please = =3E changethe strange characters on the top line to the =40 sign=2E You = can = =3E alsolook up the X-Original-From=3A line in the mail header=2E =3E = =3E E-mail to subscribers=3A CHEMISTRY=40ccl=2Enet or use=3A =3E http=3A//www=2Eccl=2Enet/cgi-bin/ccl/send=5Fccl=5Fmessage =3E = =3E E-mail to administrators=3A CHEMISTRY-REQUEST=40ccl=2Enet or use =3E http=3A//www=2Eccl=2Enet/cgi-bin/ccl/send=5Fccl=5Fmessage =3E = =3E Subscribe/Unsubscribe=3A = =3E http=3A//www=2Eccl=2Enet/chemistry/sub=5Funsub=2Eshtml =3E = =3E Before posting=2C check wait time at=3A http=3A//www=2Eccl=2Enet =3E = =3E Job=3A http=3A//www=2Eccl=2Enet/jobs = =3E Conferences=3A = =3E http=3A//server=2Eccl=2Enet/chemistry/announcements/conferences/ =3E Search Messages=3A http=3A//www=2Eccl=2Enet/chemistry/searchccl/inde= x=2Eshtml =3E = =3E If your mail bounces from CCL with 5=2E7=2E1 error=2C check=3A =3E http=3A//www=2Eccl=2Enet/spammers=2Etxt =3E = =3E RTFI=3A http=3A//www=2Eccl=2Enet/chemistry/aboutccl/instructions/ =3E = =3E = =3E From owner-chemistry@ccl.net Thu Nov 19 18:20:00 2009 From: "Andrew Orry andy-*-molsoft.com" To: CCL Subject: CCL: Workshop: Modern Drug Target Crystallography and Structure Based Drug Discovery Message-Id: <-40728-091119173807-16193-0V6HxAoqYkc5lVQ12Cluyw() server.ccl.net> X-Original-From: Andrew Orry Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Thu, 19 Nov 2009 14:32:08 -0800 MIME-Version: 1.0 Sent to CCL by: Andrew Orry [andy=-=molsoft.com] Dear All, MolSoft LLC ( www.molsoft.com ) and q.e.d. life science discoveries, inc., are conducting a joint two day workshop on Dec 14-15, 2009 at the Molsoft LLC facility in La Jolla, CA USA entitled "Modern Drug Target Crystallography and Structure Based Drug Design". The course will be taught by two experts in the field: Dr. Bernhard Rupp, crystallography textbook author and president of q.e.d. life science discoveries, and Dr. Ruben Abagyan, founder of Molsoft LLC and Professor of Pharmacology at the University of California San Diego, Skaggs School of Pharmacy and Pharmaceutical Sciences. The provided course materials include a copy of the new and highly acclaimed textbook Biomolecular Crystallography: Principles, Practice, and Applications to Structural Biology. For more information please see: http://www.ruppweb.org/workshops/Molsoft_2009.htm -- Andrew Orry Ph.D. Senior Scientist MolSoft LLC 3366 North Torrey Pines Court Suite 300 La Jolla, CA 92037 U S A Phone: (858) 625-2000 (x108) Fax: (858) 625-2888 www.molsoft.com Latest ICM News: www.molsoft.com/news.html From owner-chemistry@ccl.net Thu Nov 19 20:21:00 2009 From: "luisfer:-:edu.xunta.es" To: CCL Subject: CCL:G: G IRC run goes in same direction Message-Id: <-40729-091119180320-26071-w+dTjz201F7JN2S6XgtaRw _ server.ccl.net> X-Original-From: Content-Disposition: inline Content-Language: gl Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=iso-8859-1 Date: Fri, 20 Nov 2009 00:03:05 +0100 MIME-Version: 1.0 Sent to CCL by: [luisfer]=[edu.xunta.es] Dear Jeff=2E Are you sure that the optimized Transition Structure that you use for IR= C calculations has one and only one imaginary vibration frequency=3F=2E Best regards=2E =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D Luis F=2E R=2E V=E1zquez Obradoiro de Qu=EDmica Te=F3rica e Computacional Real Sociedad Espa=F1ola de Qu=EDmica=2E Grupo de F=EDsica At=F3mica y M= olecular Sociedade Portuguesa de Qu=EDmica=2E Divi=E7ao de Qu=EDmica F=EDsica R=FAa Tornos=2C 21=2C piso 3 15007 A Coru=F1a Tel=2E +34 676 300 472 Correo-e luisfer=40edu=2Exunta=2Ees =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D ----- Mensaxe orixinal ----- De=3A =22Jeff Woodford jwoodfor=5D=3D=5Beou=2Eedu=22 =3Cowner-chemistry=40= ccl=2Enet=3E Data=3A M=E9rcores=2C Novembro 18=2C 2009 10=3A57 pm Asunto=3A CCL=3AG=3A G IRC run goes in same direction =3E = =3E Sent to CCL by=3A =22Jeff Woodford=22 =5Bjwoodfor=3A=5F=3Aeou=2Eedu=5D= =3E My guess is that you aren=27t at a true transition state=2E Is the = =3E imaginaryfrequency very small in magnitude=3F This same thing has = =3E happened to me when =3E I don=27t use tight convergence criterion for calculating the hessia= n=2C =3E resulting in numerical error for the rotational/translational modes = =3E and a =3E spurious =22imaginary=22 frequency=2E When I tighten the convergenc= e = =3E criterion=2Cthe imaginary frequency goes away=2E =3E = =3E Just a guess=2E =3E = =3E -Jeff =3E = =3E Jeffrey N=2E Woodford =3E Associate Professor of Chemistry =3E Eastern Oregon University =3E Tel=3A 541-962-3321 =3E Fax=3A 541-962-3873 =3E = =3E -----Original Message----- =3E =3E From=3A owner-chemistry+jwoodfor=3D=3Deou=2Eedu=5D=5F=5Bccl=2Ene= t =3E =5Bmailto=3Aowner-chemistry+jwoodfor=3D=3Deou=2Eedu=5D=5F=5Bccl=2Ene= t=5D On Behalf Of = =3E Peter M =3E Burger burger=7E=7Echemie=2Euni-hamburg=2Ede =3E Sent=3A Wednesday=2C November 18=2C 2009 10=3A06 AM =3E To=3A Woodford=2C Jeffrey N = =3E Subject=3A CCL=3AG=3A G IRC run goes in same direction =3E = =3E = =3E Sent to CCL by=3A =22Peter M Burger=22 =5Bburger**chemie=2Euni-hambu= rg=2Ede=5D =3E Hello=2C =3E = =3E I noticed that the following question was asked before here but did = =3E not find =3E a = =3E conclusive answer=2E =3E = =3E So what can be done if an IRC run in g03 goes in the same direction = =3E for both =3E = =3E the reverse and forward keywords=3F =3E = =3E Regards = =3E = =3E Peterhttp=3A//www=2Eccl=2Enet/cgi- =3E bin/ccl/send=5Fccl=5Fmessagehttp=3A//www=2Eccl=2Enet/chemistry/sub=5F= unsub=2Eshtmlhttp=3A//www=2Eccl=2Enet/spammers=2Etxt =3E = =3E -=3D This is automatically added to each message by the mailing = =3E script =3D- =3E To recover the email address of the author of the message=2C please = =3E changethe strange characters on the top line to the =40 sign=2E You = can = =3E alsolook up the X-Original-From=3A line in the mail header=2E =3E = =3E E-mail to subscribers=3A CHEMISTRY=40ccl=2Enet or use=3A =3E http=3A//www=2Eccl=2Enet/cgi-bin/ccl/send=5Fccl=5Fmessage =3E = =3E E-mail to administrators=3A CHEMISTRY-REQUEST=40ccl=2Enet or use =3E http=3A//www=2Eccl=2Enet/cgi-bin/ccl/send=5Fccl=5Fmessage =3E = =3E Subscribe/Unsubscribe=3A = =3E http=3A//www=2Eccl=2Enet/chemistry/sub=5Funsub=2Eshtml =3E = =3E Before posting=2C check wait time at=3A http=3A//www=2Eccl=2Enet =3E = =3E Job=3A http=3A//www=2Eccl=2Enet/jobs = =3E Conferences=3A = =3E http=3A//server=2Eccl=2Enet/chemistry/announcements/conferences/ =3E Search Messages=3A http=3A//www=2Eccl=2Enet/chemistry/searchccl/inde= x=2Eshtml =3E = =3E If your mail bounces from CCL with 5=2E7=2E1 error=2C check=3A =3E http=3A//www=2Eccl=2Enet/spammers=2Etxt =3E = =3E RTFI=3A http=3A//www=2Eccl=2Enet/chemistry/aboutccl/instructions/ =3E = =3E = =3E