From owner-chemistry@ccl.net Thu Apr 13 02:37:00 2006 From: "Reaz Uddin riaasuddin..yahoo.com" To: CCL Subject: CCL: Making a seminar/lecture on Medicinal-Computational chemistry Message-Id: <-31505-060413022558-15671-S1sQQce0T8Zp8BRk/PXGFg{}server.ccl.net> X-Original-From: "Reaz Uddin" Date: Thu, 13 Apr 2006 02:25:57 -0400 Sent to CCL by: "Reaz Uddin" [riaasuddin]|[yahoo.com] Hi all,, I am in need to deliever a seminar on Medicinal-computational chemistry, its tools, methods and its application. This topic is mainly focused on the application of computers in drug design and discovery. For this, I want some useful links which contain the material for making an interactive and very informative seminar on this topic.. but in a short time.. If anybody has the links or related material then please respond me earliest. Thanks, emai: riaasuddin|a|yahoo.com From owner-chemistry@ccl.net Thu Apr 13 04:16:01 2006 From: "Marhoefer, R \(Richard\) Richard.Marhoefer(_)intervet.com" To: CCL Subject: CCL: Free software for drug design? ..and flexibility descriptors Message-Id: <-31506-060412143205-28061-PdULFzC6YswvX2dF6WYsXw*server.ccl.net> X-Original-From: "Marhoefer, R \(Richard\)" Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C65E57.7D852620" Date: Wed, 12 Apr 2006 19:35:27 +0200 MIME-Version: 1.0 Sent to CCL by: "Marhoefer, R \(Richard\)" [Richard.Marhoefer ~~ intervet.com] This is a multi-part message in MIME format. ------_=_NextPart_001_01C65E57.7D852620 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi all, =20 DDT stands for "Drug Discovery Today" =20 A database for journal abbreviations can be found at = http://www.ncbi.nlm.nih.gov/. Choose "Journals" in the search drop down = menu at the upper left hand side. =20 Richard =20 ________________________________=20 Dr. Richard J. Marh=F6fer=20 BioChemInformatics Scientist=20 Intervet Innovation GmbH=20 Drug Discovery / BioChemInformatics=20 Zur Propstei, 55270 Schwabenheim, Germany=20 E-mail: richard.marhoefer_-_intervet.com=20 Phone: +49 6130 948-204=20 Fax: +49 6130 948-517=20 Intervet is an Akzo Nobel Company=20 -----Original Message----- > From: Gustavo Mercier [mailto:gamercier_-_yahoo.com]=20 Sent: Mittwoch, 12. April 2006 14:29 To: Marhoefer, R (Richard) Subject: Re: CCL: Free software for drug design? ..and flexibility = descriptors Hi! You sent this message to the CCL but I am not familiar with the journal = "DDT". Could you spell out the full name? Thanks! G. Mercier "Marhoefer, R (Richard) Richard.Marhoefer^intervet.com" = wrote:=20 Sent to CCL by: "Marhoefer, R \(Richard\)" = [Richard.Marhoefer_+_intervet.com] Dear Marc, a number of free programs and/or open source programs for some of the = desired application areas are listed in: J.W. Geldenhuys, K.E. Gaasch, M. Watson, D. Allen, C.J. van der Schyf = (2006) Optimizing the use of open-source software applications in drug = discovery. DDT 11, 127-132. Richard ________________________________ Dr. Richard J. Marh=EF=BF=BDfer BioChemInformatics Scientist Intervet Innovation GmbH Drug Discovery / BioChemInformatics Zur Propstei, 55270 Schwabenheim, Germany E-mail: richard.marhoefer^-^intervet.com Phone: +49 6130 948-204 Fax: +49 6130 948-517 Intervet is an Akzo Nobel Company > -----Original Message----- > From: owner-chemistry^-^ccl.net [mailto:owner-chemistry^-^ccl.net]=20 > Sent: Montag, 27. M=EF=BF=BDrz 2006 12:15 > To: Marhoefer, R (Richard) > Subject: CCL: Free software for drug design? ..and=20 > flexibility descriptors >=20 >=20 > Sent to CCL by: Marc Baaden [baaden%x%smplinux.de] >=20 > Dear All, >=20 > concerning techniques like molecular dynamics, Monte Carlo or=20 > implementations of ab initio approaches there are a number of=20 > freely available programs for the academic community. I=20 > wonder whether similar 'free' (non-commercial) software=20 > exists for drug design? In particular for the following tasks: > - virtual screening > - pharmacophore modeling > - receptor mapping > - QSAR and 3D-QSAR > - Shape alignments > - ComFa-like methods > My focus would be more on exploring these approaches then on=20 > applying them in a production environment on huge projects.=20 > I'd be very grateful for suggestions and comments. >=20 > One more specific request: what type of molecular or atomic=20 > descriptors do exist for conformational flexibility? >=20 > Thank you very much in advance, > Marc Baaden >=20 > --=20 > Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris > mailto:baaden|a|smplinux.de - http://www.baaden.ibpc.fr > FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217 >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing=20 > script =3D- To recover the email address of the author of the=20 > message, please change the strange characters on the top line=20 > to the ^-^ sign. You can also look up the X-Original-From: line=20 > in the mail header.> Conferences:=20 > http://server.ccl.net/chemistry/announcements/conferences/ >=20 > Search Messages: http://www.ccl.net/htdig (login: ccl,=20 > Password: search)>=20 > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+ >=20 >=20 >=20 >=20 -------------------------------------- This message, including attachments, is confidential and may be = privileged. If you are not an intended recipient, please notify the sender then = delete and destroy the original message and all copies. You should not copy, = forward and/or disclose this message, in whole or in part, without permission of the sender. -------------------------------------- -=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-- Gustavo A. Mercier, Jr. MD,PhD Baylor University Medical Center Radiology American Radiology Associates 712 N. Washington, Suite 101 Dallas, TX 75246 214-826-8822 214-826-9792 fax gamercier_-_yahoo.com = =20 -------------------------------------- This message, including attachments, is confidential and may be privileged. If you are not an intended recipient, please notify the sender then delete and destroy the original message and all copies. You should not copy, forward and/or disclose this message, in whole or in part, without permission of the sender. -------------------------------------- ------_=_NextPart_001_01C65E57.7D852620 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Message
Hi=20 all,
 
DDT=20 stands for "Drug Discovery Today"
 
A=20 database for journal abbreviations can be found at http://www.ncbi.nlm.nih.gov/. = Choose=20 "Journals" in the search drop down menu at the upper left hand=20 side.
 
Richard
 

________________________________
Dr. Richard J.=20 Marh=F6fer
BioChemInformatics Scientist
Intervet Innovation GmbH
Drug Discovery /=20 BioChemInformatics
Zur Propstei, 55270 Schwabenheim, Germany =
E-mail:=20 richard.marhoefer_-_intervet.com
Phone: +49 6130 948-204
Fax:     = +49 6130=20 948-517
Intervet is=20 an Akzo Nobel Company

-----Original Message-----
From: Gustavo Mercier=20 [mailto:gamercier_-_yahoo.com]
Sent: Mittwoch, 12. April 2006=20 14:29
To: Marhoefer, R (Richard)
Subject: Re: CCL: = Free=20 software for drug design? ..and flexibility=20 descriptors

Hi!

You sent this message to the = CCL but=20 I am not familiar with the journal "DDT". Could you spell out the full=20 name?

Thanks!
G. Mercier

"Marhoefer, R (Richard)=20 Richard.Marhoefer^intervet.com" <owner-chemistry_-_ccl.net> = wrote:
Sent=20 to CCL by: "Marhoefer, R \(Richard\)"=20 [Richard.Marhoefer_+_intervet.com]

Dear Marc,

a number = of free=20 programs and/or open source programs for some of the desired = application areas=20 are listed in:

J.W. Geldenhuys, K.E. Gaasch, M. Watson, D. = Allen, C.J.=20 van der Schyf (2006) Optimizing the use of open-source software = applications=20 in drug discovery. DDT 11,=20 127-132.

Richard

________________________________
Dr. = Richard=20 J. Marh=EF=BF=BDfer
BioChemInformatics Scientist
Intervet = Innovation=20 GmbH
Drug Discovery / BioChemInformatics
Zur Propstei, 55270=20 Schwabenheim, Germany
E-mail: = richard.marhoefer^-^intervet.com
Phone:=20 +49 6130 948-204
Fax: +49 6130 948-517
Intervet is an Akzo Nobel = Company



> -----Original Message-----
> From:=20 owner-chemistry^-^ccl.net [mailto:owner-chemistry^-^ccl.net]
> = Sent:=20 Montag, 27. M=EF=BF=BDrz 2006 12:15
> To: Marhoefer, R = (Richard)
>=20 Subject: CCL: Free software for drug design? ..and
> = flexibility=20 descriptors
>
>
> Sent to CCL by: Marc Baaden=20 [baaden%x%smplinux.de]
>
> Dear All,
>
> = concerning=20 techniques like molecular dynamics, Monte Carlo or
> = implementations of=20 ab initio approaches there are a number of
> freely available = programs=20 for the academic community. I
> wonder whether similar 'free'=20 (non-commercial) software
> exists for drug design? In = particular for=20 the following tasks:
> - virtual screening
> - = pharmacophore=20 modeling
> - receptor mapping
> - QSAR and 3D-QSAR
> = - Shape=20 alignments
> - ComFa-like methods
> My focus would be more = on=20 exploring these approaches then on
> applying them in a = production=20 environment on huge projects.
> I'd be very grateful for = suggestions=20 and comments.
>
> One more specific request: what type of = molecular or atomic
> descriptors do exist for conformational=20 flexibility?
>
> Thank you very much in advance,
> = Marc=20 Baaden
>
> --
> Dr. Marc Baaden - Institut de = Biologie=20 Physico-Chimique, Paris
> mailto:baaden|a|smplinux.de -=20 http://www.baaden.ibpc.fr
> FAX: +33 15841 5026 - Tel: +33 15841 = 5176 ou=20 +33 609 843217
>
>
>
> -=3D This is = automatically=20 added to each message by the mailing
> script =3D- To recover = the email=20 address of the author of the
> message, please change the = strange=20 characters on the top line
> to the ^-^ sign. You can also look = up the=20 X-Original-From: line
> in the mail header.> Conferences: =
>=20 http://server.ccl.net/chemistry/announcements/conferences/
> =
>=20 Search Messages: http://www.ccl.net/htdig (login: ccl,
> = Password:=20 search)>
>=20 -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
> = -+-+-+-+-+
>
>
>
>=20
--------------------------------------
This message, including=20 attachments, is confidential and may be privileged.
If you are not = an=20 intended recipient, please notify the sender then delete
and = destroy the=20 original message and all copies. You should not copy, = forward
and/or=20 disclose this message, in whole or in part, without permission = of
the=20 sender.
--------------------------------------



-=3D = This is=20 automatically added to each message by the mailing script =3D-
To = recover the=20 email address of the author of the message, please change
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E-mail to = subscribers:=20 CHEMISTRY_-_ccl.net or=20 use:
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-+-+-+-+-+-+-+= -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+





--
Gustavo A. Mercier, Jr. MD,PhD
Baylor University Medical = Center
Radiology
American Radiology Associates
712 N. Washington, Suite 101
Dallas, TX 75246
214-826-8822
214-826-9792 fax
gamercier_-_yahoo.com 

--------------------------------------
This message, including attachments, is confidential and may be privileged. If you are not an intended recipient, please notify the sender then delete and destroy the original message and all copies. You should not copy, forward and/or disclose this message, in whole or in part, without permission of the sender.
--------------------------------------
------_=_NextPart_001_01C65E57.7D852620-- From owner-chemistry@ccl.net Thu Apr 13 09:20:00 2006 From: "Steve Williams willsd]_[appstate.edu" To: CCL Subject: CCL:G: G03W Message-Id: <-31507-060413081117-28637-yDgS9mZjHVKqnOFjb4M0/Q * server.ccl.net> X-Original-From: Steve Williams Content-transfer-encoding: 7bit Content-type: text/plain; format=flowed; charset=ISO-8859-1 Date: Thu, 13 Apr 2006 08:10:17 -0400 MIME-version: 1.0 Sent to CCL by: Steve Williams [willsd^^^appstate.edu] I just got a copy of single computer license copy G03W (could not afford the unix version), and am trying to decide what machine to install it on. I'd like to get some advice on this: 1) Will this take advantge of the 64-bit version of windows xp running on a 64-bit chip (say an opteron) so as to avoid the 2GB file size limitation of G98 and G98W? 2) If installed on dual core chip machine (perhaps a pentium D) will %nproc=2 do the "right thing" and use both cores? 3) If installed on a two processor motherboard machine will %nproc=2 do the right thing? If both processors were dual core, would %nproc=4 actually use all four cores? Note that this is not a special multiprocessor version of G03W, nor is LINDA available. Thanks, Steve Williams From owner-chemistry@ccl.net Thu Apr 13 09:55:00 2006 From: "Ricky Shen hxhgxy2:_:163.com" To: CCL Subject: CCL:G: Cube file Message-Id: <-31508-060413093909-15521-XnKohn8YlVvx9BI8GNcv6g/./server.ccl.net> X-Original-From: "Ricky Shen" Date: Thu, 13 Apr 2006 09:39:08 -0400 Sent to CCL by: "Ricky Shen" [hxhgxy2++163.com] Hi, Only Computing the Laplacian of the density, The error will be appear. the cube file can't be archived. My input file: %rwf=csc,-1 %nosave %chk=csc %mem=750mb P b3lyp/6-31g* geom=check guess=read Cube=(laplacian,Fine) No title specified 0 1 csc.cube And the error: PGFIO-F-217/formatted read/unit=5/attempt to read past end of file. File name = /home/swain/sc/Gau-3661.inp formatted, sequential access record = 12 In source file dencub.f, at line number 366 At Linux OS, both G98 and G03 have error, but it not appear at Windows OS. From owner-chemistry@ccl.net Thu Apr 13 11:07:00 2006 From: "Jozsef Csontos jozsefcsontos,creighton.edu" To: CCL Subject: CCL:G: G03W Message-Id: <-31509-060413103412-18477-8JEhQrscR1FaR/YPzFvZDQ++server.ccl.net> X-Original-From: Jozsef Csontos Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Thu, 13 Apr 2006 09:33:55 -0500 Mime-Version: 1.0 Sent to CCL by: Jozsef Csontos [jozsefcsontos,,creighton.edu] Hi, I have no experience with the windows version, but considering the linux one the answers are yes for your questions. My guess is that the same is true for the windows version. Best wishes, Jozsef On Thu, 2006-04-13 at 09:32 -0400, Steve Williams willsd]_[appstate.edu wrote: > Sent to CCL by: Steve Williams [willsd^^^appstate.edu] > I just got a copy of single computer license copy G03W (could not afford > the unix version), and am trying to decide what machine to install it > on. I'd like to get some advice on this: > 1) Will this take advantge of the 64-bit version of windows xp running > on a 64-bit chip (say an opteron) so as to avoid the 2GB file size > limitation of G98 and G98W? > 2) If installed on dual core chip machine (perhaps a pentium D) will > %nproc=2 do the "right thing" and use both cores? > 3) If installed on a two processor motherboard machine will %nproc=2 do > the right thing? If both processors were dual core, would %nproc=4 > actually use all four cores? > Note that this is not a special multiprocessor version of G03W, nor is > LINDA available. > Thanks, > Steve Williams> > > -- Jozsef Csontos, Ph.D. Department of Biomedical Sciences Creighton University, Omaha, NE From owner-chemistry@ccl.net Thu Apr 13 11:41:01 2006 From: "Goedele Roos groos*vub.ac.be" To: CCL Subject: CCL: bindings energy with BSSE or in solvent? Message-Id: <-31510-060413074456-27135-tNhtP8lFy+gZ2nGWmXSn7g^^server.ccl.net> X-Original-From: Goedele Roos Date: Thu, 13 Apr 2006 12:49:46 +0200 (CEST) Sent to CCL by: Goedele Roos [groos- -vub.ac.be] Dear list, It seems one has to choose between the calculation of the bindingsenergy with BSSE or in solvent. Because no BSSE is available for a continuum solvent model (PCM), or am I wrong here? What would you choose and why: gasphase with BSSE? Or solvent phase without BSSE and calculating all the three components apart: E(complex); E(proteine); E(ligand)? Thank you for answering my question! Best regards , Goedele Drs. Goedele Roos Dienst Algemene Chemie (ALGC) Vrije Universiteit Brussel (VUB) Pleinlaan 2 B-1050 Brussels Tel: 0032-2-629 35 16 Fax: 0032-2-629 33 17 From owner-chemistry@ccl.net Thu Apr 13 13:45:00 2006 From: "Shobe, David dshobe#,#sud-chemieinc.com" To: CCL Subject: CCL: FW: bindings energy with BSSE or in solvent? Message-Id: <-31511-060413134438-10702-FHIwgotlDKAzjE/ATwZh2Q*|*server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 13 Apr 2006 19:44:34 +0200 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [dshobe##sud-chemieinc.com] You might not be able to combine BSSE and PCM in a single calculation, but you can still calculate a BSSE correction in one calculation and calculate the solvation energy in another. --David Shobe, Ph.D., M.L.S. Süd-Chemie, Inc. phone (502) 634-7409 fax (502) 634-7724 Don't bother flaming me: I'm behind a firewall. -----Original Message----- > From: owner-chemistry|,|ccl.net [mailto:owner-chemistry|,|ccl.net] Sent: Thursday, April 13, 2006 12:00 PM To: Shobe, David Subject: CCL: bindings energy with BSSE or in solvent? Sent to CCL by: Goedele Roos [groos- -vub.ac.be] Dear list, It seems one has to choose between the calculation of the bindingsenergy with BSSE or in solvent. Because no BSSE is available for a continuum solvent model (PCM), or am I wrong here? What would you choose and why: gasphase with BSSE? Or solvent phase without BSSE and calculating all the three components apart: E(complex); E(proteine); E(ligand)? Thank you for answering my question! Best regards , Goedele Drs. Goedele Roos Dienst Algemene Chemie (ALGC) Vrije Universiteit Brussel (VUB) Pleinlaan 2 B-1050 Brussels Tel: 0032-2-629 35 16 Fax: 0032-2-629 33 17http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. Thank you. From owner-chemistry@ccl.net Thu Apr 13 17:17:00 2006 From: "Young Leh youngleh#gmail.com" To: CCL Subject: CCL:G: Cu2+ BLYP Calculation Error Message-Id: <-31512-060413154201-17601-5hcU0zDhFuajiVe+FtCt4Q/a\server.ccl.net> X-Original-From: "Young Leh" Date: Thu, 13 Apr 2006 15:41:53 -0400 Sent to CCL by: "Young Leh" [youngleh]~[gmail.com] Dear CCLer, I ran a single point Cu2+ calculation at BLYP/6-31G* level using Gaussian and got error message shown below: Matrix for removal 18 Erem= -1639.28113846461 Crem= 0.000D+00 Density matrix breaks symmetry, PCut= 1.00D-04 Density has only Abelian symmetry. EnCoef did 100 forward-backward iterations Matrix for removal 6 Erem= -1639.28153822889 Crem= 0.000D+00 >>>>>>>>>> Convergence criterion not met. SCF Done: E(UB-LYP) = -1639.27987110 A.U. after 129 cycles Convg = 0.2246D-01 -V/T = 2.0019 S**2 = 0.7504 Annihilation of the first spin contaminant: S**2 before annihilation 0.7504, after 0.7500 Convergence failure -- run terminated. Error termination via Lnk1e in c:\program files\G03W\l502.exe at Thu Apr 13 12:39:27 2006. Job cpu time: 0 days 0 hours 1 minutes 6.0 seconds. File lengths (MBytes): RWF= 11 Int= 0 D2E= 0 Chk= 1 Scr= 1 What could be the reason? Thanks for the input. Young Leh From owner-chemistry@ccl.net Thu Apr 13 19:02:01 2006 From: "Yan Zhao yzhao * chem.umn.edu" To: CCL Subject: CCL:G: Cu2+ BLYP Calculation Error Message-Id: <-31513-060413185432-29089-vL31YAvN8dGXH07XH4ohFg]*[server.ccl.net> X-Original-From: Yan Zhao Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 12 Apr 2006 14:22:36 -0500 MIME-Version: 1.0 Sent to CCL by: Yan Zhao [yzhao{}chem.umn.edu] You got a SCF convergence problem, try the keyword SCF=QC. Yan Young Leh youngleh#gmail.com wrote: > Sent to CCL by: "Young Leh" [youngleh]~[gmail.com] > Dear CCLer, > > I ran a single point Cu2+ calculation at BLYP/6-31G* level using Gaussian and got error message shown below: > > Matrix for removal 18 Erem= -1639.28113846461 Crem= 0.000D+00 > Density matrix breaks symmetry, PCut= 1.00D-04 > Density has only Abelian symmetry. > EnCoef did 100 forward-backward iterations > Matrix for removal 6 Erem= -1639.28153822889 Crem= 0.000D+00 > >>>>>>>>>> Convergence criterion not met. > SCF Done: E(UB-LYP) = -1639.27987110 A.U. after 129 cycles > Convg = 0.2246D-01 -V/T = 2.0019 > S**2 = 0.7504 > Annihilation of the first spin contaminant: > S**2 before annihilation 0.7504, after 0.7500 > Convergence failure -- run terminated. > Error termination via Lnk1e in c:\program files\G03W\l502.exe at Thu Apr 13 12:39:27 2006. > Job cpu time: 0 days 0 hours 1 minutes 6.0 seconds. > File lengths (MBytes): RWF= 11 Int= 0 D2E= 0 Chk= 1 Scr= 1 > > What could be the reason? Thanks for the input. > > Young Leh> > > >