From owner-chemistry@ccl.net Fri Oct 14 04:24:00 2005 From: "FyD fyd+*+u-picardie.fr" To: CCL Subject: CCL: partial charge fitting - free QM package Message-Id: <-29603-051014023718-30423-+NAU8ywlZjXnktzQb7gkzw|server.ccl.net> X-Original-From: FyD Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 14 Oct 2005 08:37:05 +0200 MIME-Version: 1.0 Sent to CCL by: FyD [fyd\a/u-picardie.fr] Quoting "Spencer Ericksen spencer_ericksen!^!hotmail.com" : As previsouly said, you can use GAMESS or NWChem with the R.E.D. interface http://www.u-picardie.fr/labo/lbpd/RED/ R.E.D. allows to automatically set multi-orientation and multiconformation RESP or ESP fit. Regards, Francois -- * F.-Y. Dupradeau * DMAG EA 3901 & Faculte de Pharmacie, Amiens, France **** http://www.u-picardie.fr/labo/lbpd/FyD.htm From owner-chemistry@ccl.net Fri Oct 14 06:40:00 2005 From: "Sandro Cosconati sa.cosco- -virgilio.it" To: CCL Subject: CCL: W:Q5, proQ and Qavetr for Irix6.5 Message-Id: <-29604-051014063843-16823-bVB5DW9DUlvanPFIGAVsNQ+*+server.ccl.net> X-Original-From: "Sandro Cosconati" Sent to CCL by: "Sandro Cosconati" [sa.cosco() virgilio.it] Dear all, I'd like to run some MD simulations with Q5 package. Unfortunately, on Q web site the IRIX6.5 executables of Q5 package, proq and Qavetr are not provided . I was wondering if there was someone who could send me these executables compiled for IRIX6.5. Alternatively, I would be grateful if someone could send me at least the executables of proq and Qavetr compiled for IRIX6.4 or Irix6.5. Thanks in advance for all your help Best Regards Sandro From owner-chemistry@ccl.net Fri Oct 14 08:19:00 2005 From: "Richard Wong richard_mw_wong\a/yahoo.com.sg" To: CCL Subject: CCL: Frequency scaling factor! Message-Id: <-29605-051014064813-22955-TztHUtZM/l5oKD8sFswJng[]server.ccl.net> X-Original-From: Richard Wong Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-522769940-1129283288=:31123" Date: Fri, 14 Oct 2005 17:48:08 +0800 (CST) MIME-Version: 1.0 Sent to CCL by: Richard Wong [richard_mw_wong|-|yahoo.com.sg] --0-522769940-1129283288=:31123 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Here are another two references related to frequencies scaling factors for DFT methods: (1) "Vibrational Frequency Prediction Using Density Functional Theory", M.W. Wong, Chem. Phys. Lett. 256 (1996) 391-399. (2) "The Prediction of Vibrational Frequencies of Inorganic Molecules Using Density Functional Theory", I. Bytheway and M.W. Wong, Chem. Phys. Lett. 282 (1998) 219-226. Richard "Bende Attila bende|s3.itim-cj.ro" wrote: Sent to CCL by: Bende Attila [bende,;,s3.itim-cj.ro] Hi everybody! I would appreciate if you could give me some detailed lists or articles about vibrational frequency scaling factor values. ex. Method (DFT, ab initio) / Basis set / Scaling factor. In particularly, I'm interested in B3LYP/6-31G and B3LYP/6-31G** cases, but also for other case could come in useful for me. Thanks in advance -- Dr. Bende Attila (PhD) Senior Researcher III *********************************************************************** National Institute of R&D of Izotopic and Molecular Tehnology Str. Donath nr.71-103, P.O.Box 700 Cluj-Napoca, Ro-400293, Romania Phone:+40-264-584037, int 216, Fax: +40-264-420042 e-mail: bende:-:s3.itim-cj.ro, AttlBende:-:yahoo.co.uk web page: http://w3.itim-cj.ro/~bende ***********************************************************************http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--------------------------------- Do you Yahoo!? New and Improved Yahoo! Mail - 1GB free storage! --0-522769940-1129283288=:31123 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit

Here are another two references related to frequencies scaling factors for DFT methods:

 

(1) "Vibrational Frequency Prediction Using Density Functional Theory", M.W. Wong, Chem. Phys. Lett. 256 (1996) 391-399.

(2) "The Prediction of Vibrational Frequencies of Inorganic Molecules Using Density Functional Theory", I. Bytheway and M.W. Wong, Chem. Phys. Lett. 282 (1998) 219-226.

 

Richard


"Bende Attila bende|s3.itim-cj.ro" <owner-chemistry]_[ccl.net> wrote:

Sent to CCL by: Bende Attila [bende,;,s3.itim-cj.ro]
Hi everybody!

I would appreciate if you could give me some detailed lists or articles about
vibrational frequency scaling factor values.
ex. Method (DFT, ab initio) / Basis set / Scaling factor.

In particularly, I'm interested in B3LYP/6-31G and B3LYP/6-31G** cases, but
also for other case could come in useful for me.

Thanks in advance

--
Dr. Bende Attila (PhD)
Senior Researcher III

***********************************************************************
National Institute of R&D of Izotopic and Molecular Tehnology
Str. Donath nr.71-103, P.O.Box 700
Cluj-Napoca, Ro-400293, Romania
Phone:+40-264-584037, int 216, Fax: +40-264-420042
e-mail: bende:-:s3.itim-cj.ro, AttlBende:-:yahoo.co.uk
web page: http://w3.itim-cj.ro/~bende
***********************************************************************


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New and Improved Yahoo! Mail - 1GB free storage! --0-522769940-1129283288=:31123-- From owner-chemistry@ccl.net Fri Oct 14 08:54:01 2005 From: "Peter Gannett pgannett[#]hsc.wvu.edu" To: CCL Subject: CCL: partial charge fitting - free QM package Message-Id: <-29606-051014080322-10559-GK4I6qI88Tzaqh6Caabf/A^_^server.ccl.net> X-Original-From: "Peter Gannett" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII Date: Fri, 14 Oct 2005 08:03:58 -0400 Mime-Version: 1.0 Sent to CCL by: "Peter Gannett" [pgannett : hsc.wvu.edu] Spencer: Try GAMESS available at http://www.msg.ameslab.gov/GAMESS/GAMESS.html Generally, people get charges from 6-31g level (or better). For small molecules, these calculations do not take very long. Of course, if you have a large number of molecules, computational time could become an issue. If you just want charges for the purpose of screening then perhaps you can just use Gasteiger partial atomic charge method. Pete >>> owner-chemistry=ccl.net 10/13 1:05 PM >>> Sent to CCL by: "Spencer Ericksen" [spencer_ericksen**hotmail.com] Hello CCLers: I am constructing drug molecules to dock into a receptor using molecular mechanics forcefield representation of atoms. The drug molecules were built in Sybyl and partial charges were first added using the Gasteiger-Marsili charges by default. I then performed an AM1 MOPAC calculation to derive Mulliken charges which were differed to some extent. I do not currently have a program to perform higher level ab initio calculations from which tto derive better charges. Where may I obtain a free QM program that performs ab initio calculations with acceptable basis sets for small organic molecules from which to derive MM partial charges? Are higher level QM calculations necessary to fit a good set of partial charges--even when solvent effects are not included in typical calculations (gas phase)? What is the most common technique for partial charge assignment is used for high-throughput in silico screening by docking when millions of ligands are used? Spencer Ericksen Dept. of Physiology UW-Madison ericksen---physiology.wisc.eduhttp://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 Fri Oct 14 10:09:00 2005 From: "ReichertD||mir.wustl.edu" To: CCL Subject: CCL: partial charge fitting - free QM package Message-Id: <-29607-051014100214-22290-4NriMEQoALExe8ZnPf2V7Q-,-server.ccl.net> X-Original-From: ReichertD-*-mir.wustl.edu Content-type: multipart/related; Boundary="0__=09BBFA09DFDF355C8f9e8a93df938690918c09BBFA09DFDF355C" Date: Fri, 14 Oct 2005 09:02:07 -0500 MIME-Version: 1.0 Sent to CCL by: ReichertD _ mir.wustl.edu --0__=09BBFA09DFDF355C8f9e8a93df938690918c09BBFA09DFDF355C Content-type: multipart/alternative; Boundary="1__=09BBFA09DFDF355C8f9e8a93df938690918c09BBFA09DFDF355C" --1__=09BBFA09DFDF355C8f9e8a93df938690918c09BBFA09DFDF355C Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: quoted-printable Hi, One of the reputed "best " methods are AM1-BCC charges, see: (1) Jakalian, A.; Bush, B. L.; Jack, D. B.; Bayly, C. I. Fast, effici= ent generation of high-quality atomic charges. AM1-BCC model: I. Method. J.= Comp. Chem. 2000, 21, 132-146. (2) Jakalian, A.; Jack, D. B.; Bayly, C. I. Fast, efficient generatio= n of high-quality atomic charges. AM1-BCC model: II. parameterization and validation. J. Comp. Chem. 2002, 23, 1623-1641. OpenEyes software has a program QUACPAC which can generate these charge= s very quickly. In my personal experience with docking, I've never found = a huge difference between charge calculation methods, overall it's way mo= re important to make sure that all the charges were generated the same way= . that's my $0.02, -david David Reichert, Ph.D. Asst. Professor Radiology Washington University School of Medicine 510 S. Kingshighway, Campus Box 8225 St Louis, MO 63110 e-mail: reichertd(_)wustl.edu voice: (314) 362-8461 fax: (314) 362-9940 = "Spencer Ericksen = spencer_ericksen! = ^!hotmail.com" = To = Sent by: = cc owner-chemistry(_)c = cl.net Subj= ect CCL: partial charge fitting - fr= ee QM package = 10/13/2005 12:05 = PM = = = Please respond to = "CCL Subscribers" = = = = Sent to CCL by: "Spencer Ericksen" [spencer_ericksen**hotmail.com] Hello CCLers: I am constructing drug molecules to dock into a receptor using molecula= r mechanics forcefield representation of atoms. The drug molecules were built in Sybyl and partial charges were first added using the Gasteiger-Marsi= li charges by default. I then performed an AM1 MOPAC calculation to deriv= e Mulliken charges which were differed to some extent. I do not currentl= y have a program to perform higher level ab initio calculations from whic= h tto derive better charges. Where may I obtain a free QM program that performs ab initio calculatio= ns with acceptable basis sets for small organic molecules from which to de= rive MM partial charges? Are higher level QM calculations necessary to fit a good set of partial= charges--even when solvent effects are not included in typical calculat= ions (gas phase)? What is the most common technique for partial charge assignment is used= for high-throughput in silico screening by docking when millions of ligands= are used? Spencer Ericksen Dept. of Physiology UW-Madison ericksen---physiology.wisc.edu -=3D This is automatically added to each message by the mailing script = =3D- To recover the email address of the author of the message, please chang= ehttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-= + = --1__=09BBFA09DFDF355C8f9e8a93df938690918c09BBFA09DFDF355C Content-type: text/html; charset=US-ASCII Content-Disposition: inline Content-transfer-encoding: quoted-printable

Hi,
One of the reputed "best " methods are AM1-BCC charges, see:<= br>
(1) Jakalian, A.; Bush, B. L.; Jack, D. B.; Bayly, C. I. Fast, efficien= t generation of high-quality atomic charges. AM1-BCC model: I. Method. = J. Comp. Chem. 2000, 21, 132-146.
(2) Jakalian, A.; Jack, D. B.; Bayly, C. I. Fast, efficient generation = of high-quality atomic charges. AM1-BCC model: II. parameterization and= validation. J. Comp. Chem. 2002, 23, 1623-1641.

OpenEyes software has a program QUACPAC which can generate these charge= s very quickly. In my personal experience with docking, I've never foun= d a huge difference between charge calculation methods, overall it's wa= y more important to make sure that all the charges were generated the s= ame way.
that's my $0.02,
-david

David Reichert, Ph.D.
Asst. Professor Radiology
Washington University School of Medicine
510 S. Kingshighway, Campus Box 8225
St Louis, MO 63110

e-mail: reichertd(_)wustl.edu
voice: (314) 362-8461
fax: (314) 362-9940
3D"Inactive"Spencer Ericksen spencer_ericksen!^!hotmail.com" <owne= r-chemistry(_)ccl.net>


=
          "Spencer Ericksen spencer_ericksen!^!hotma= il.com" <owner-chemistry(_)ccl.net>
          Sent by: owner-chemistry(_)ccl.net

          10/13/2005 12:05 PM =
          Please respond to
          "CCL Subscribers" <chemistry(_)ccl.net>

 =

To
3D""
"Reichert, David E. " <reichertd(_)= mir.wustl.edu>

cc
3D""

Subject
3D""
CCL: partial charge fitting - free QM package
=3D""3D""<= /td>


Sent to CCL by: "Spencer Ericksen" [spencer_ericksen**hotmail= .com]
Hello CCLers:

I am constructing drug molecules to dock into a receptor using molecula= r
mechanics forcefield representation of atoms.  The drug molecules = were built
in Sybyl and partial charges were first added using the Gasteiger-Marsi= li
charges by default.  I then performed an AM1 MOPAC calculation to = derive
Mulliken charges which were differed to some extent.  I do not cur= rently
have a program to perform higher level ab initio calculations from whic= h tto
derive better charges.

Where may I obtain a free QM program that performs ab initio calculatio= ns
with acceptable basis sets for small organic molecules from which to de= rive
MM partial charges?

Are higher level QM calculations necessary to fit a good set of partial=
charges--even when solvent effects are not included in typical calculat= ions
(gas phase)?

What is the most common technique for partial charge assignment is used= for
high-throughput in silico screening by docking when millions of ligands= are
used?

Spencer Ericksen

Dept. of Physiology UW-Madison
ericksen---physiology.wisc.edu



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= --1__=09BBFA09DFDF355C8f9e8a93df938690918c09BBFA09DFDF355C-- --0__=09BBFA09DFDF355C8f9e8a93df938690918c09BBFA09DFDF355C Content-type: image/gif; name="graycol.gif" Content-Disposition: inline; filename="graycol.gif" Content-ID: <10__=09BBFA09DFDF355C8f9e8a(_)msnotes.wustl.edu> Content-transfer-encoding: base64 R0lGODlhEAAQAKECAMzMzAAAAP///wAAACH5BAEAAAIALAAAAAAQABAAAAIXlI+py+0PopwxUbpu ZRfKZ2zgSJbmSRYAIf4fT3B0aW1pemVkIGJ5IFVsZWFkIFNtYXJ0U2F2ZXIhAAA7 --0__=09BBFA09DFDF355C8f9e8a93df938690918c09BBFA09DFDF355C Content-type: image/gif; name="pic23655.gif" Content-Disposition: inline; filename="pic23655.gif" Content-ID: <20__=09BBFA09DFDF355C8f9e8a(_)msnotes.wustl.edu> Content-transfer-encoding: base64 R0lGODlhWABDALP/AAAAAK04Qf79/o+Gm7WuwlNObwoJFCsoSMDAwGFsmIuezf///wAAAAAAAAAA AAAAACH5BAEAAAgALAAAAABYAEMAQAT/EMlJq704682770RiFMRinqggEUNSHIchG0BCfHhOjAuh EDeUqTASLCbBhQrhG7xis2j0lssNDopE4jfIJhDaggI8YB1sZeZgLVA9YVCpnGagVjV171aRVrYR RghXcAGFhoUETwYxcXNyADJ3GlcSKGAwLwllVC1vjIUHBWsFilKQdI8GA5IcpApeJQt8L09lmgkH LZikoU5wjqcyAMMFrJIDPAKvCFletKSev1HBw8KrxtjZ2tvc3d5VyKtCKW3jfz4uMKmq3xu4N0nK BVoJQmx2LGVOmrqNjjJf2hHAQo/eDwJGTKhQMcgQEEAnEjFS98+RnW3smGkZU6ncCWav/4wYOnAI TihRL/4FEwbp28BXMMcoscQCVxlepL4IGDSCyJyVQOu0o7CjmLN50OZlqWmyFy5/6yBBuji0AxFR M00oQAqNIstqI6qKHUsWRAEAvagsmfUEAImyxgbmUpJk3IklNUtJOUAVLoUr1+wqDGTE4zk+T6FG uQb3SizBCwatiiUgCBN8vrz+zFjVyQ8FWkOlg4NQiZMB5QS8QO3mpOaKnL0Z2EKvNMSILEThKhCg zMKPVxYJh23qm9KNW7pArPynMqZDiErsTMqI+LRi3QAgkFUbXpuFKhSYZALd0O5RKa2z9EYKBbpb qxIKsjUPRgD7I2XYV6wyrOw92ykExP8NW4URhknC5dKGE4v4NENQj2jXjmfNgOZDaXb5glRmXQ33 YEWQYNcZFnrYcIQLNzyTFDQNkXIff0ExVlY4srziQk43inZgL4rwxxINMvpFFAz1KOODHiu+4aEw NEjFl5B3JIKWKF3k6I9bfUGp5ZZcdunll5IA4cuHvQQJ5gcsoCWOOUwgltIwAKRxJgbIkJAQZEq0 2YliZnpZZ4BH3CnYOXldOUOfQoYDqF1LFHbXCrO8xmRsfoXDXJ6ChjCAH3QlhJcT6VWE6FCkfCco CgrMFsROrIEX3o2whVjWDjoJccN3LdggSGXLCdLEgHr1lyU3O3QxhgohNKXJCWv8JQr/PDdaqd6w 2rj1inLiGeiCJoDspAoQlYE6QWLSECehcWIYxIQES6zhbn1iImTHEQyqJ4eIxJJoUBc+3CbBuwZE V5cJPPkIjFDdeEabQbd6WgICTxiiz0f5dBKquXF6k4senwEhYGnKEFJeGrxUZy8dB8gmAXI/sPvH ESfCwVt5hTgYiqQqtdRNHQIU1PJ33ZqmzgE90OwLaoJcnMop1WiMmgkPHQRIrwgFuNV90A3doNKT mrKIN07AnGcI9BQjhCBN4RfA1qIZnMqorJCogKfGQnxSCDilTVIA0yl5ciTovgLuBDKFUDE9aQcw 9SA+rjSNf9/M1gxrj6VwDTS0IUSElMzBfsj0NFXR2kwsV1A5IF1grLgLL/r1R40BZEnuBWgmQEyb jqRwSAt6bqMCOFkvKFN2GPPkUzIm/SCF8z8pVzpbjVnMsy0vOr1hw3SaSRUhpY09v0z0J1FnwzPl fmh+xl4WtR0zGu24I4KbMQm3lnVu2oNWxI9W/lcyzA+mCKF4DBikxb/+UWtOGRiFP8qEwAayIgIA Ow== --0__=09BBFA09DFDF355C8f9e8a93df938690918c09BBFA09DFDF355C Content-type: image/gif; name="ecblank.gif" Content-Disposition: inline; filename="ecblank.gif" Content-ID: <30__=09BBFA09DFDF355C8f9e8a(_)msnotes.wustl.edu> Content-transfer-encoding: base64 R0lGODlhEAABAIAAAAAAAP///yH5BAEAAAEALAAAAAAQAAEAAAIEjI8ZBQA7 --0__=09BBFA09DFDF355C8f9e8a93df938690918c09BBFA09DFDF355C-- From owner-chemistry@ccl.net Fri Oct 14 10:43:00 2005 From: "Nuno Palma nuno.palma-,-bial.com" To: CCL Subject: CCL: Help on G03 error: "Incomplete coordinate system" Message-Id: <-29608-051014100041-21908-9xyYAYifUDsT/salIbgO7g#,#server.ccl.net> X-Original-From: "Nuno Palma" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 14 Oct 2005 14:13:29 +0100 MIME-Version: 1.0 Sent to CCL by: "Nuno Palma" [nuno.palma]-[bial.com] Dear all, I'm getting a recurrent error during geometry optimization (PM3 level) jobs, using Gaussian G03W. I can't figure out what this error means and couldn't find any helping information on the manuals or the web. So I'm hopping someone from this forum could have any helpfull hint. The system I'm studying is composed of two reactant molecules, which are kept from falling appart, using coordination constraints (therefore, these are partial geom optimizations). The optimization runs apparently OK for a number of steps, but eventually it stops with the following message Incomplete coordinate system. Try restarting with Geom=Check Guess=Read Opt=(ReadFC,NewRedundant) Incomplete coordinate system. Error termination via Lnk1e in c:\programas\chemistry\G03W\l103.exe at Fri Oct 14 10:37:31 2005. Job cpu time: 0 days 0 hours 13 minutes 21.0 seconds. File lengths (MBytes): RWF= 12 Int= 0 D2E= 0 Chk= 8 Scr= 1 I tried inputing the molecule specification in both cartesian (using ONION with some coordinates frozen) or Z-matrix (imposing constraints with opt=ModRedundant). However, I got the above error in both situations. Anyone help, please? Nuno ** nuno.palma:+:bial.com ** From owner-chemistry@ccl.net Fri Oct 14 11:57:00 2005 From: "John Akapulco akapulco]^[ouvaton.org" To: CCL Subject: CCL: W:AM1 parameters for B, Zn in Gaussian03 Message-Id: <-29609-051014101508-675-uKxuO21mT4w7naKs8bEBYw]^[server.ccl.net> X-Original-From: "John Akapulco" Sent to CCL by: "John Akapulco" [akapulco[*]ouvaton.org] Dear all, Running a job using Gaussian03 at the semi-emperical AM1 level for a B, C, H, Zn containing molecule, I do not got the references for the AM1 parameters. Furthermore, I do not think that parameters for B and Zn have been implemented in AM1 / GAUSSIAN03. Do you ? (please, indicate the reference ;-) . I did severall tests : changing Zn by a transition metal as Ru leads also to a complete job (there are no AM1 parameters for TM, such as Ru !!!). What does Gaussian AM1 ? Best regards. John Akapulco akapulco%x%ouvaton.org From owner-chemistry@ccl.net Fri Oct 14 13:20:00 2005 From: "Wendy Cornell wdcornell===yahoo.com" To: CCL Subject: CCL: Spring 2006 ACS in Atlanta - COMP Division "Paradigm Shift" Award Competition Message-Id: <-29610-051014131649-19637-lf9JTXZ1wkgJpwvfis/z6Q : server.ccl.net> X-Original-From: Wendy Cornell Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1247607508-1129306599=:19675" Date: Fri, 14 Oct 2005 09:16:39 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Wendy Cornell [wdcornell~~yahoo.com] --0-1247607508-1129306599=:19675 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit New Award Symposium The COMP Division of ACS is pleased to announce a new award symposium -- the "Thomas Kuhn Paradigm Shift Award Competition" -- sponsored by OpenEye Scientific Software. This symposium will take place at the Spring 2006 National Meeting in Atlanta and will focus on talks relevant to drug discovery. Abstracts can be submitted on the OASYS web site (oasys.acs.org) and four will be selected for 40 minute presentations to take place during a half-day symposium at the national meeting. Abstracts not selected for the symposium competition can be moved into the General Oral Drug Discovery symposium (which is always well attended!) if desired. Criteria and Prize A panel of judges will select the winning presentation with the speaker awarded a $1000 prize. Talks will be judged on the novelty of viewpoint, the cogency of argument and the potential impact if the speaker's paradigm were to become widely accepted. About Thomas Kuhn In the 1940's, while still a graduate student, Thomas Kuhn wrote a monograph on the nature of scientific revolution that was to become the most influential document on the nature of science of the Twentieth Century. Published in 1962 as 'The Structure of Scientific Revolutions', Kuhn described what he saw as the "essential tension" between established ideas, or paradigms, and the new; scientific progress arose by conflict and not consensus. The "Thomas Kuhn Paradigm Shift Award" is designed as an opportunity for speakers to present views at odds with perceived wisdom, with particular emphasis on application to the science of drug discovery. --------------------------------- Yahoo! Music Unlimited - Access over 1 million songs. Try it free. --0-1247607508-1129306599=:19675 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit

New Award Symposium
The COMP Division of ACS is pleased to announce a new award symposium -- the "Thomas Kuhn Paradigm Shift Award Competition" -- sponsored by OpenEye Scientific Software.  This symposium will take place at the Spring 2006 National Meeting in Atlanta and will focus on talks relevant to drug discovery.  Abstracts can be submitted on the OASYS web site (oasys.acs.org) and four will be selected for 40 minute presentations to take place during a half-day symposium at the national meeting.  Abstracts not selected for the symposium competition can be moved into the General Oral Drug Discovery symposium (which is always well attended!) if desired.

Criteria and Prize
A panel of judges will select the winning presentation with the speaker awarded a $1000 prize.  Talks will be judged on the novelty of viewpoint, the cogency of argument and the potential impact if the speaker's paradigm were to become widely accepted.

About Thomas Kuhn
In the 1940's, while still a graduate student, Thomas Kuhn wrote a monograph on the nature of scientific revolution that was to become the most influential document on the nature of science of the Twentieth Century.  Published in 1962 as 'The Structure of Scientific Revolutions', Kuhn
described what he saw as the "essential tension" between established ideas, or paradigms, and the new; scientific progress arose by conflict and not consensus. The "Thomas Kuhn Paradigm Shift Award" is designed as an opportunity for speakers to present views at odds with perceived wisdom, with particular emphasis on application to the science of drug discovery.


Yahoo! Music Unlimited - Access over 1 million songs. Try it free. --0-1247607508-1129306599=:19675-- From owner-chemistry@ccl.net Fri Oct 14 13:55:00 2005 From: "Christopher Cramer cramer],[chem.umn.edu" To: CCL Subject: CCL: partial charge fitting - free QM package Message-Id: <-29611-051014131958-19877-LRbbDWRzzo+25dnwQ0ritg{}server.ccl.net> X-Original-From: Christopher Cramer Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed Date: Fri, 14 Oct 2005 11:19:50 -0500 Mime-Version: 1.0 (Apple Message framework v623) Sent to CCL by: Christopher Cramer [cramer^^chem.umn.edu] While on the subject of mapped charges, I believe that Brian Shoichet has been having good successing using CMx charges for docking studies. The CMx models (x = 1, 2, 3, etc. by generation) involve a charge mapping to take class II (population analysis) or class III (fit to computed observable) charges to class IV charges (fit to experimental observables). The original paper on the philosophy and methods was: Storer, J. W.; Giesen, D. J.; Cramer, C. J.; Truhlar, D. G. "Class IV Charge Models: A New Semiempirical Approach in Quantum Chemistry" J. Comput.-Aid. Mol. Des. 1995, 9, 87. A particularly recent paper is Kelly, C. P.; Cramer, C. J.; Truhlar, D. G. "Accurate Partial Atomic Charges for High-Energy Molecules Using Class IV Charge Models with the MIDI! Basis Set" Theor. Chem. Acc. 2005, 113, 133. Chris Cramer On Oct 14, 2005, at 9:02 AM, ReichertD||mir.wustl.edu wrote: > > Hi, > One of the reputed "best " methods are AM1-BCC charges, see: > > (1) Jakalian, A.; Bush, B. L.; Jack, D. B.; Bayly, C. I. Fast, > efficient > generation of high-quality atomic charges. AM1-BCC model: I. Method. J. > Comp. Chem. 2000, 21, 132-146. > (2) Jakalian, A.; Jack, D. B.; Bayly, C. I. Fast, efficient > generation of > high-quality atomic charges. AM1-BCC model: II. parameterization and > validation. J. Comp. Chem. 2002, 23, 1623-1641. > > OpenEyes software has a program QUACPAC which can generate these > charges > very quickly. In my personal experience with docking, I've never found > a > huge difference between charge calculation methods, overall it's way > more > important to make sure that all the charges were generated the same way -- Christopher J. Cramer University of Minnesota Department of Chemistry 207 Pleasant St. SE Minneapolis, MN 55455-0431 -------------------------- Phone: (612) 624-0859 || FAX: (612) 626-2006 Mobile: (612) 597-5275 cramer!A!pollux.chem.umn.edu http://pollux.chem.umn.edu/~cramer (website includes information about the textbook "Essentials of Computational Chemistry: Theories and Models, 2nd Edition") From owner-chemistry@ccl.net Fri Oct 14 15:27:00 2005 From: "Troy Wymore wymore|*|psc.edu" To: CCL Subject: CCL: PSC WORKSHOP: COMPUTATIONAL BIOPHYSICS WORKSHOP Message-Id: <-29612-051014151531-32285-B8wCCyWKriKNzpWHVDtERQ,server.ccl.net> X-Original-From: Troy Wymore Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Fri, 14 Oct 2005 14:10:48 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: Troy Wymore [wymore/./psc.edu] ************************************************** PITTSBURGH SUPERCOMPUTING CENTER NATIONAL RESOURCE FOR BIOMEDICAL SUPERCOMPUTING WORKSHOP This workshop is funded by a grant to the PSC from the NIH National Center for Research Resources. The grant provides tuition, hotel, supercomputing time, and workshop materials for US academic participants. COMPUTATIONAL BIOPHYSICS WORKSHOP Nov. 28 - Dec. 1 Application Deadline: October 24 Primary Instructor: Prof. Klaus Schulten (UIUC) www.psc.edu/biomed/training/workshops/2005/NAMD/index.html The workshop will explore physical models and computational approaches used for the simulation of biological systems and the investigation of their function at an atomic level. The course will be based on case studies including the properties of membranes and membrane proteins, mechanisms of molecular motors, trafficking in the living cell through water and ion channels, and signaling pathways. Relevant physical concepts, mathematical techniques, and computational methods will be introduced, including force fields and algorithms used in molecular modeling, molecular dynamics simulations on parallel computers and steered molecular dynamics simulations. The workshop is designed for graduate students and postdoctoral researchers in computational and/or biophysical fields who seek to extend their research skills to include computational and theoretical expertise, as well as other researchers interested in theoretical and computational biophysics. Theory sessions in the morning will be followed by hands-on computer labs in the afternoon in which students will be able to set up and run simulations. For specific details, including an electronic application form, see: www.psc.edu/biomed/training/workshops/2005/NAMD/index.html Please direct any questions about the workshop to Dr. Troy Wymore (wymore[a]psc.edu). From owner-chemistry@ccl.net Fri Oct 14 17:04:01 2005 From: "TJ O Donnell tjo;;acm.org" To: CCL Subject: CCL: Where can you publish articles on software? Message-Id: <-29613-051014170009-4544-cISwCrpdtj1+sFWQsg6kXg() server.ccl.net> X-Original-From: "TJ O'Donnell" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 14 Oct 2005 14:00:01 -0700 MIME-Version: 1.0 Sent to CCL by: "TJ O'Donnell" [tjo^-^acm.org] Well, I've been staying out of this fray, but having just started to market a closed-source product, this issue has been on my mind a lot over the past year. Warren writes: > The only way to publish software in a scientifically robust manner is to > share source code, and that means publishing via the internet in an > open-access/open-source fashion. Anything short of that amounts to > issuing unproven claims based on limited empirical tests regarding what > a given program allegedly does. What is that called outside of science? > Advertising! And as such, I agree that it does not belong in a > scientific journal. Either you publish software with source code and > stand behind it, or you are blowing smoke and quite *literally* hiding > something -- no matter how noble your intent. This is a rather extreme statement, that needs to be tempered, IMHO. Hiding source code is NOT tantamount to deception, as is implied above. Results of a program are, perhaps, the only ~scientifically~ relevant aspect of a program; the only useful effect of it; and the only thing that must be subject to scientific scrutiny. Results MUST be carefully considered, reviewed and verified. If they are in error, one must consider the assumptions, theory, algorithms and, of course, the code behind those erroneous results. Do instrument designers publish their schematics (I honestly don't know). Does Varian, et. al.? Does that make those instruments tantamount to scientific fraud? Absolutely not! Why? Because the RESULTS (spectra, etc.) are subject to intense scientific scrutiny. Let me just finish by saying that I subject my own programs to intense scientific scrutiny and welcome such from my users. It becomes my responsibility to correct errors, as any experimentalist does. For those who may be interested, my new work is at: http://www.gnova.com/ Sincerely, TJ O'Donnell, Ph.D. gNova Scientific Software http://www.gnova.com/ From owner-chemistry@ccl.net Fri Oct 14 17:39:00 2005 From: "Alexander Martins Silva alex.msilva*uol.com.br" To: CCL Subject: CCL: TCP connect error Message-Id: <-29614-051014172843-19084-JreSi3nAslcdyDEdyKto3A##server.ccl.net> X-Original-From: Alexander Martins Silva Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 14 Oct 2005 18:35:52 -0300 MIME-Version: 1.0 Sent to CCL by: Alexander Martins Silva [alex.msilva]~[uol.com.br] Hi, When I try to execute a Gamess parallel job at 2 nodes of my cluster with the command line ../ddikick.x ../gamess.01.x exam01 -ddi 2 2 node01:cpus=1 node02:cpus=1 -scr , I've got the following error message: Distributed Data Interface kickoff program. Initiating 2 compute processes on 2 nodes to run the following command: ../gamess.01.x exam01 TCP connect error: ECONNREFUSED. TCP: Connect failed. server -> node01:34910. A fatal error occurred on DDI Process 2. TCP connect error: ECONNREFUSED. TCP: Connect failed. server -> node01:34910. A fatal error occurred on DDI Process 0. Permission denied. ddikick.x: Timed out while waiting for DDI processes to check in. ddikick.x: Fatal error detected. The error is most likely to be in the application, so check for input errors, disk space, memory needs, application bugs, etc. ddikick.x will now clean up all processes, and exit... ddikick.x: Sending kill signal to DDI processes. ddikick.x: Execution terminated due to error(s). what happens? How can I fix this? Thanks is advance, Alexander. From owner-chemistry@ccl.net Fri Oct 14 18:13:01 2005 From: "Rick Venable rvenable[*]pollux.cber.nih.gov" To: CCL Subject: CCL: Cremer & Pople Fortran source Message-Id: <-29615-051014173236-19436-2Zfa5gyNog1JtCXC6xptig{:}server.ccl.net> X-Original-From: Rick Venable Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Fri, 14 Oct 2005 17:30:07 -0400 MIME-Version: 1.0 Sent to CCL by: Rick Venable [rvenable#,#pollux.cber.nih.gov] I'm looking for Fortran source code which computes the C+P puckering parameters for 5- and esp. 6-membered rings; source code or other tips would be greatly appreciated. Regards, ------------------------------------- Rick Venable 29/500 FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable AT nih*gov ALT email: rvenable AT speakeasy*org ------------------------------------- www.redcross.org From owner-chemistry@ccl.net Fri Oct 14 18:49:00 2005 From: "Sengen Sun sengensun*|*yahoo.com" To: CCL Subject: CCL: Condensed Fukui Functions Message-Id: <-29616-051014182715-27711-6bGMPAXmeivE5Zxarqjj4w|*|server.ccl.net> X-Original-From: Sengen Sun Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Fri, 14 Oct 2005 14:27:06 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Sengen Sun [sengensun**yahoo.com] There are some limitations of any FMO-derived parameters no matter how you make them mathematically. There are surely useful patterns between the reactivity and FMOs or their derived indexes. But these patterns like empirical rules do not have a definite generality, and fail from time to time as pointed by authors such as Hehre & Dewar (as I remember). Therefore, there is no cure in some cases. Any FMO-derived parameters may not be used to make any firm conclusions that cannot be experimentally verfified. Sengen ----------------------------------------- > From: b wafaa Date: Mon, 10 Oct 2005 14:51:37 +0200 (CEST) Subject: CCL: Condensed Fukui Functions Sent to CCL by: b wafaa [wafaab2=yahoo.fr] --0-1144409699-1128948697=:17669 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear CCLers, We have some problems in the prediction of reactivity when we calculate condensed Fukui functions with the finite difference approximation using N, N-1 and N+1 systems. In your opinion, what is the best method for the calculation of these indexes ? Which population analysis do you suggest ? Sincerely __________________________________ Start your day with Yahoo! - Make it your home page! http://www.yahoo.com/r/hs From owner-chemistry@ccl.net Fri Oct 14 20:45:00 2005 From: "Warren DeLano warren],[delsci.com" To: CCL Subject: CCL: Where can you publish articles on software? Message-Id: <-29617-051014203102-2577-RstgpTIZJ8kwwNTOjeoywQ]~[server.ccl.net> X-Original-From: "Warren DeLano" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 14 Oct 2005 17:31:22 -0700 MIME-Version: 1.0 Sent to CCL by: "Warren DeLano" [warren*|*delsci.com] > From: TJ O'Donnell [mailto:tjo*acm.org] > > Warren writes: > > The only way to publish software in a scientifically robust > manner is > > to share source code, and that means publishing via the > internet in an > > open-access/open-source fashion. Anything short of that amounts to > > issuing unproven claims based on limited empirical tests regarding > > what a given program allegedly does. What is that called > outside of science? > > Advertising! And as such, I agree that it does not belong in a > > scientific journal. Either you publish software with > source code and > > stand behind it, or you are blowing smoke and quite > *literally* hiding > > something -- no matter how noble your intent. > This is a rather extreme statement, that needs to be tempered, IMHO. > Hiding source code is NOT tantamount to deception, as is > implied above. No -- let me clarify -- I do not imply that closed-source is tantamount to deception. It is simply non-disclosure -- a willful holding back of pertinent helpful information. It is tantamount to saying "trust me" -- I have correctly applied chemistry, physics, math, and computer science to create a working solution to your problem. Thorough testing of closed-source code can of course lay an empirical foundation for extending such trust, and testing is equally necessary with open-source code. But testing alone is not the same as disclosing an implementation that can itself be subjected to direct intellectual scrutiny. While there are valid personal, economic, political, legal, practical, and insitutional reasons for not disclosing source code, I challenge anyone to come up with a compelling scientific reason for why source code should not be disclosed -- when possible -- to enable understanding, reproduction, verification, and extension of computational advances. Is there ever a legitimate *purely scientific* reason for settling with empirical evidence alone (just test results) when mathematical proof is itself attainable (via inspection of source code)? I cannot think of any. Or are we all agreed that making source code available is the *scientific* ideal to which we should all aspire? If so, then when we do not make source available, we should certainly have some compelling non-scientific reason for holding it back, and as honest scientists, we must realize that doing so will have the effect of limiting the value and impact of our work -- at least from a scientific standpoint. Intellectual advances are either shared or lost, and software implementations are no exception to this. Cheers, Warren PS. A trivial concrete illustration: I write some function called "add_two_numbers" and share it will my colleagues. And for the millions of pairs of numbers they test it on, it returns the sum. So much so good. But without source, no one can even be sure that there isn't some untested pair of numbers for which it fails. Now I share the source: def add_two_numbers(a,b): return a+b > From that point on, everyone can sleep well knowing for certain that my function will always return the sum of two numbers, since the implementation is public and exact. Science can progress because Warren has re-implemented addition. Hooray! On the other hand, if the source was reveald to be: def add_two_numbers(a,b): if (a == 1823723) and (b == 8374723): return 6 else: return a+b Then everyone would immediately know for certain that my function is flawed and needs to be fixed. Could testing have found this? Assuming that the inputs are 32-bits wide, then there are 2^64 combinations of possible inputs with only one flaw. 2^64 is far too many inputs to practially examine, so this flaw would almost certainly never have been found through testing. Thus, even in the simplest function, it is possible to introduce a flaw that cannot be found through rigorous regression testing. Admittedly this example is contrived, but it isn't hard to see how testing can easily miss subtle problems that could well be identified through critical analysis of source code. -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:warren*delsci.com