From chemistry-request@server.ccl.net Wed Apr 23 14:25:24 2003 Received: from messenger.csusb.edu ([139.182.2.65]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3NIPOa09355 for ; Wed, 23 Apr 2003 14:25:24 -0400 Received: from conversion-daemon.messenger.csusb.edu by messenger.csusb.edu (iPlanet Messaging Server 5.2 HotFix 1.12 (built Feb 13 2003)) id <0HDT00A017G890@messenger.csusb.edu> for CHEMISTRY@ccl.net; Wed, 23 Apr 2003 11:31:23 -0700 (PDT) Received: from csusb.edu (localhost [127.0.0.1]) by messenger.csusb.edu (iPlanet Messaging Server 5.2 HotFix 1.12 (built Feb 13 2003)) with ESMTP id <0HDT00I617G91S@messenger.csusb.edu> for CHEMISTRY@ccl.net; Wed, 23 Apr 2003 11:31:21 -0700 (PDT) Received: from [66.51.218.229] by messenger.csusb.edu (mshttpd); Wed, 23 Apr 2003 10:31:21 -0800 Date: Wed, 23 Apr 2003 10:31:21 -0800 From: kcousins@csusb.edu Subject: Chime for Mac problems? To: CHEMISTRY@ccl.net Message-id: <1fd821deeb.1deeb1fd82@csusb.edu> MIME-version: 1.0 X-Mailer: iPlanet Messenger Express 5.2 HotFix 1.12 (built Feb 13 2003) Content-type: text/plain; charset=us-ascii Content-language: en Content-transfer-encoding: 7BIT Content-disposition: inline X-Accept-Language: en Priority: normal Sorry if this is a little off subject . . . I have created some pdb format files using babel1.6 for linux. These files look fine when I open them in chem3D or with RasMac. But when I open them with the latest chime plugin for Mac (2.6SP3, using netscape 4.75) I get a black background only. I've tried using the MDL menu to change colors/displays, and the file still looks black. My Chime works fine when viewing files from web servers. Any ideas? Is this a known limitation of Chime/mac (that it won't read some formats of pdb files?)_ Or is it because my file is on my local computer, and not being served by a mime-type knowlegable server? By the way, the MDL site does not say anything about this on their "limitations" page. Kimberley R. Cousins Associate Professor of Chemistry California State University, San Bernardino http://chem.csusb.edu/~kcousins kcousins@csusb.edu From chemistry-request@server.ccl.net Wed Apr 23 21:57:00 2003 Received: from GWIA.HSC.WVU.EDU ([157.182.105.18]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3O1v0a19763 for ; Wed, 23 Apr 2003 21:57:00 -0400 Received: from HSC-DOM5-MTA by GWIA.HSC.WVU.EDU with Novell_GroupWise; Wed, 23 Apr 2003 21:57:00 -0400 Message-Id: X-Mailer: Novell GroupWise Internet Agent 6.0.2 Date: Wed, 23 Apr 2003 21:56:54 -0400 From: "Peter Gannett" To: , Subject: Re: CCL:Chemistry and architecture relationships Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h3O1v0a19764 Miquel: Sounds like a tough audience. Here are a few that come to mind and might help. Hydrocarbons: Tetrahedran, housane, basketane, cubane (just search on the names to get structures for but you can get a good idea of what they look like from their names). There are also the catenanes (two rings, one passing through the other). Others come to mind but need a bit of imagination, for example, DNA looks like a spiral staircase. Hope this helps. Pete Gannett >>> Miquel Solà 04/19/03 10:14AM >>> Dear CCLers, I have to give a talk to graduate students in Architecture on tools used for chemists to display molecular properties. I would like to start the introduction with a reference to relationships between chemistry and architecture. I know only one clear example of this relation which is the C60 molecule called buckminsterfullerene for its similarity with the geodesic domes made by the architect Richard Buckminster Fuller. Do you know other examples? I will post a summary if there is interest. Thanks in advance for your answers. Best regards, Miquel -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- Miquel Solà Institut de Química Computacional Universitat de Girona Campus Montilivi 17071 Girona, CATALONIA (Spain) Phone +34.972.41.89.12 Cellular-Phone: +34.626.163.580 FAX +34.972.41.83.56 World Wide Web: http://iqc.udg.es/~miquel/mike.html e-mail: miquel.sola@udg.es -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- From chemistry-request@server.ccl.net Wed Apr 23 15:04:20 2003 Received: from pscuxc.psc.edu ([128.182.66.177]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3NJ4Ka10500 for ; Wed, 23 Apr 2003 15:04:20 -0400 Received: from pscuxc.psc.edu (localhost.psc.edu [127.0.0.1]) by pscuxc.psc.edu (8.12.9/8.12.5) with ESMTP id h3NJ4KDl001739 for ; Wed, 23 Apr 2003 15:04:20 -0400 (EDT) Received: from localhost (wymore@localhost) by pscuxc.psc.edu (8.12.9/8.12.8/Submit) with ESMTP id h3NJ4Kr2026729 for ; Wed, 23 Apr 2003 15:04:20 -0400 (EDT) Date: Wed, 23 Apr 2003 15:04:19 -0400 (EDT) From: Troy Wymore To: Subject: PSC Summer Workshop: Modeling from Protein Sequence to Structure (update) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLer's I apologize for the repeated posting. Their was a minor error in the admissions form about tuition to the workshop that is now corrected and was correct under the financial page. 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. More information is listed below and on the workshop website. *************************************************** PSC BIOMEDICAL INITIATIVE WORKSHOP 2003 MODELING FROM PROTEIN SEQUENCE TO STRUCTURE: COMPUTATIONAL TOOLS FOR STRUCTURE PREDICTION June 2-5 Application Deadline: April 30 Primary Instructor: Prof. Charles Brooks (Scripps) This workshop will introduce researchers to computational tools (the MMTSB Tool Set available at http://mmtsb.scripps.edu) aimed at predicting structure based on sequence alone, from identification of suitable homology templates, or through application of secondary-structure templated de novo folding, as well as refinement and energy calculations on "ensembles" of molecular structures. This freely available tool set comprises a perl-based library of applications that interface to the molecular modeling packages CHARMM and Amber, and the MONSSTER package for protein structure prediction. Participants in the workshop will be presented lectures on molecular modeling theory and practice, protein structure prediction, loop modeling and energy-based structure refinement. Advanced sampling methods such as replica-exchange molecular dynamics, as utilized in structure prediction algorithms, will be discussed. Practical tutorials exploring the use and application of the MMTSB tool set will focus on conventional molecular mechanics calculations of energy, minimization and dynamics as well as loop modeling and refinement using replica-exchange molecular dynamics and hierarchical protein structure prediction using de novo (or secondary structure templated) folding algorithms in the MONSSTER and CHARMM packages. Web-based servers for protein sequence alignment, secondary structure prediction and homology template identification will be discussed in the context of their utility to the overall structure prediction pipeline utilizing the MMTSB Tool Set. For specific details, including an electronic application form, see: http://www.psc.edu/biomed/training/workshops/2003/proteomics/index.html If you have any questions, please contact Nancy Blankenstein at blankens@psc.edu From chemistry-request@server.ccl.net Thu Apr 24 01:14:53 2003 Received: from ns.ciac.jl.cn ([202.98.16.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3O5Eja22313 for ; Thu, 24 Apr 2003 01:14:51 -0400 Received: from zhang1 (localhost [127.0.0.1]) by ns.ciac.jl.cn (8.9.1/8.9.1) with SMTP id NAA23000; Thu, 24 Apr 2003 13:18:03 +0800 (CST) Message-Id: <200304240518.NAA23000@ns.ciac.jl.cn> From: "zjwu" To: "help@gaussian.com" CC: "chemistry@ccl.net" Subject: Re: Re: CCL:CPCM TS location X-mailer: Foxmail 4.2 [cn] Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====002_Dragon164465607246_=====" Date: Thu, 24 Apr 2003 13:13:16 +0800 This is a multi-part message in MIME format. --=====002_Dragon164465607246_===== Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 7bit Dear Dr. Hess, I mean the job failing because the structure is not the TS structure anymore. The calculation may converge but goes to different geometry which I did not want. I have tried to read force constants at cpcm calculation from either gas phase frequency calculation or Onsager frequency calculation (these frequencies are obtained based on the optimized geometry) (calculation using Onsager model works well for the TS calculation). In addition, I also tried opt=(ts,calcfc), but as you know, calcfc does not exist for cpcm. It seems g03 is possible to calculate fc at cpcm level. Hope I have made myself clear. Thank you very much for your answer. Best regards, Zhijian Wu Dear Dr. Zhijian Wu, Is this job failing because it runs out of optimization cycles? I'd need to know more details about what is going wrong before I make detailed suggestions, but one possible way to improve this calculation is to calculate the force constants in the solution phase, then use these force constants to start the transition state search. Usually the gas-phase Hessian is a good enough approximation, but in some cases where the gas-phase and solution-phase potential energy surfaces are different enough, explicitly calculating the second derivatives in the solution phase can be helpful. Incidentally, if you are using G98, the CPCM second derivatives will be performed by numerical differentiation of the analytic gradients and if you are using G03, the second derivatives will be calculated analytically. Regards, Jim Hess ++++++++++++++++++++++++++ James Hess, Ph.D. Customer Support Scientist Gaussian, Inc. e-mail: help@gaussian.com ++++++++++++++++++++++++++ On Tuesday, April 22, 2003, at 08:29 PM, zjwu wrote: >> Dear members, >> >> ?/DIV> >> >> I am trying to locate the transition state using cpcm model. The >> initial structure is from gas phase optimized transition structure >> (with correct vibrational mode). The optimization at cpcm level fails >> by the following keywords >> >> ?/DIV> >> >> #b3lyp/6-31g(d,p) opt=(ts, readfc, noeigen) scrf=(cpcm,solvent=water) >> >> ?/DIV> >> >> Do anybody has experience in cpcm transition structure calculation? >> >> ?/DIV> >> >> Thanks a lot. >> >> ?/DIV> >> >> Best regards, >> >> ?/DIV> >> >> Zhijian Wu >> Dear Dr. Zhijian Wu, Is this job failing because it runs out of optimization cycles? I'd need to know more details about what is going wrong before I make detailed suggestions, but one possible way to improve this calculation is to calculate the force constants in the solution phase, then use these force constants to start the transition state search. Usually the gas-phase Hessian is a good enough approximation, but in some cases where the gas-phase and solution-phase potential energy surfaces are different enough, explicitly calculating the second derivatives in the solution phase can be helpful. Incidentally, if you are using G98, the CPCM second derivatives will be performed by numerical differentiation of the analytic gradients and if you are using G03, the second derivatives will be calculated analytically. Regards, Jim Hess ++++++++++++++++++++++++++ James Hess, Ph.D. Customer Support Scientist Gaussian, Inc. e-mail: help@gaussian.com ++++++++++++++++++++++++++ On Tuesday, April 22, 2003, at 08:29 PM, zjwu wrote: << excerpt> Dear members, ?/DIV> I am trying to locate the transition state using cpcm model. The initial structure is from gas phase optimized transition structure (with correct vibrational mode). The optimization at cpcm level fails by the following keywords ?/DIV> #b3lyp/6-31g(d,p) opt=(ts, readfc, noeigen) scrf=(cpcm,solvent=water) ?/DIV> Do anybody has experience in cpcm transition structure calculation? ?/DIV> Thanks a lot. ?/DIV> Best regards, ?/DIV> Zhijian Wu << /excerpt> --=====002_Dragon164465607246_===== Content-Type: text/html; charset="GB2312" Content-Transfer-Encoding: 7bit

Dear Dr. Hess,

 

I mean the job failing because the structure is not the TS structure anymore. The calculation may converge but goes to different geometry which I did not want. I have tried to read force constants at cpcm calculation from either gas phase frequency calculation or Onsager frequency calculation (these frequencies are obtained based on the optimized geometry) (calculation using Onsager model works well for the TS calculation). In addition, I also tried opt=(ts,calcfc), but as you know, calcfc does not exist for cpcm. It seems g03 is possible to calculate fc at cpcm level.

 

Hope I have made myself clear.

 

Thank you very much for your answer.

 

Best regards,

 

Zhijian Wu

 

Dear Dr. Zhijian Wu,
    Is this job failing because it runs out of optimization cycles? I'd 
need to know more details about what is going wrong before I make 
detailed suggestions, but one possible way to improve this calculation 
is to calculate the force constants in the solution phase, then use 
these force constants to start the transition state search. Usually the 
gas-phase Hessian is a good enough approximation, but in some cases 
where the gas-phase and solution-phase potential energy surfaces are 
different enough, explicitly calculating the second derivatives in the 
solution phase can be helpful. Incidentally, if you are using G98, the 
CPCM second derivatives will be performed by numerical differentiation 
of the analytic gradients and if you are using G03, the second 
derivatives will be calculated analytically.
 
Regards,
Jim Hess
 
++++++++++++++++++++++++++
James Hess, Ph.D.
Customer Support Scientist
Gaussian, Inc.
e-mail: help@gaussian.com
++++++++++++++++++++++++++
 
 
On Tuesday, April 22, 2003, at 08:29 PM, zjwu wrote:
 
>>  Dear members,
>>
>>  ?/DIV>
>>
>>  I am trying to locate the transition state using cpcm model. The 
>>  initial structure is from gas phase optimized transition structure 
>>  (with correct vibrational mode). The optimization at cpcm level fails 
>>  by the following keywords
>>
>>  ?/DIV>
>>
>>  #b3lyp/6-31g(d,p) opt=(ts, readfc, noeigen) scrf=(cpcm,solvent=water)
>>
>>  ?/DIV>
>>
>>  Do anybody has experience in cpcm transition structure calculation?
>>
>>  ?/DIV>
>>
>>  Thanks a lot.
>>
>>  ?/DIV>
>>
>>  Best regards,
>>
>>  ?/DIV>
>>
>>  Zhijian Wu
>>
Dear Dr. Zhijian Wu,
 
   Is this job failing because it runs out of optimization cycles? I'd
need to know more details about what is going wrong before I make
detailed suggestions, but one possible way to improve this calculation
is to calculate the force constants in the solution phase, then use
these force constants to start the transition state search. Usually
the gas-phase Hessian is a good enough approximation, but in some
cases where the gas-phase and solution-phase potential energy surfaces
are different enough, explicitly calculating the second derivatives in
the solution phase can be helpful. Incidentally, if you are using G98,
the CPCM second derivatives will be performed by numerical
differentiation of the analytic gradients and if you are using G03,
the second derivatives will be calculated analytically.
 
 
Regards,
 
Jim Hess
 
 
++++++++++++++++++++++++++
 
James Hess, Ph.D.          
 
Customer Support Scientist
 
Gaussian, Inc.
 
e-mail: help@gaussian.com
 
++++++++++++++++++++++++++
 
 
 
On Tuesday, April 22, 2003, at 08:29 PM, zjwu wrote:
 
 
<< excerpt> Dear members,
 
 
?/DIV>
 
 
I am trying to locate the transition state using cpcm model. The
initial structure is from gas phase optimized transition structure
(with correct vibrational mode). The optimization at cpcm level fails
by the following keywords
 
 
?/DIV>
 
 
#b3lyp/6-31g(d,p) opt=(ts, readfc, noeigen) scrf=(cpcm,solvent=water)
 
 
?/DIV>
 
 
Do anybody has experience in cpcm transition structure calculation?
 
 
?/DIV>
 
 
Thanks a lot.
 
 
?/DIV>
 
 
Best regards,
 
 
?/DIV>
 
 
Zhijian Wu
 
 
<< /excerpt>
--=====002_Dragon164465607246_=====-- From chemistry-request@server.ccl.net Wed Apr 23 10:19:09 2003 Received: from correo1.us.es ([150.214.9.229]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3NEJ9a01420 for ; Wed, 23 Apr 2003 10:19:09 -0400 Received: from correo1.us.es (localhost.localdomain [127.0.0.1]) by correo1.us.es (8.11.6/8.11.1) with ESMTP id h3NFJSi29271 for ; Wed, 23 Apr 2003 16:19:28 +0100 Received: from us.es (pc13.us.es [150.214.145.103]) by correo1.us.es (8.11.6/8.11.1) with ESMTP id h3NFJO329248 for ; Wed, 23 Apr 2003 16:19:24 +0100 Sender: norge@us.es Message-ID: <3EA69F20.74D6481F@us.es> Date: Wed, 23 Apr 2003 16:11:44 +0200 From: Norge Cruz Hernandez Organization: Quimica Fisica X-Mailer: Mozilla 4.08 [en] (X11; I; OSF1 V3.2 alpha) MIME-Version: 1.0 To: chemistry@ccl.net Subject: CCL: about VASP. Content-Type: multipart/alternative; boundary="------------7C6DF1284003E2EB4979A5D2" --------------7C6DF1284003E2EB4979A5D2 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear CCLers, Does anybody have some experience compiling and using VASP in IBM SP3 machine. I would like to contact. Best regards Norge -- PhD. Norge Cruz Hernandez. Dpto. Quimica Fisica Facultad de Quimica Calle: Prof. Garcia Gonzalez Sevilla, 41012 Spain Tel: +34 954557177 (209) Fax: +34 954557174 PD. Paris, 2002. Un trabajador migratorio argelino se pasea por las calles con una pancarta que dice : "Estamos aquí porque ustedes estuvieron allá" --------------7C6DF1284003E2EB4979A5D2 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers,

Does anybody have some experience compiling and using VASP in IBM SP3 machine.
I would like to contact.

Best regards
Norge 




-- 
PhD. Norge Cruz Hernandez.
Dpto. Quimica Fisica
Facultad de Quimica
Calle: Prof. Garcia Gonzalez
Sevilla, 41012
Spain
Tel: +34 954557177 (209)
Fax: +34 954557174 

PD. Paris, 2002. Un trabajador migratorio argelino se pasea por las calles con 
una pancarta que dice :
              "Estamos aquí porque ustedes estuvieron allá"

 

--------------7C6DF1284003E2EB4979A5D2--



From chemistry-request@server.ccl.net Wed Apr 23 12:09:40 2003
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Date: Wed, 23 Apr 2003 09:55:26 +0200
From: Giulio Vistoli 
Subject: Re: CCL:about the DCD file got from NAMD
To: CCL 
Message-id: <005c01c3096d$b3cda570$424f959f@farma.unimi.it>
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References: 
 <200304211238.22753.weiz@mail.rochester.edu>

Dear wei,

To analyze the DCD files you can use also VEGA (http://www.ddl.unimi.it)!!!!

Using VEGA you can calculate not only geometrical properties (like
distances, angles, torsions), but also molecular properties (like SAS, PSA,
logP dipole, lipole, etc) and it include a graph editor to visualize and
manage the obtained results.

Best regards

Giulio Vistoli

_____________

Giulio Vistoli
Istituto di Chimica Farmaceutica e Tossicologica
Viale Abruzzi, 42
I-20131 Milano
Italia
Tel. +39-02-50317545
Fax +39-02-50317565
giulio.vistoli@unimi.it
http://www.ddl.unimi.it




From chemistry-request@server.ccl.net Wed Apr 23 20:30:08 2003
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Reply-To: 
From: "Donald Keidel" 
To: 
Subject: Gaussian test001.com file not completing
Date: Wed, 23 Apr 2003 17:29:55 -0700
Organization: UCR
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Hello all,

 

I have reinstalled Gaussian 98 rev.A.9 on the same computer that it used
to be installed on (and working before I formatted and changed the hard
drive - 5400 rpm hard drive) and tested the installation using the
test001.com file.  This same file runs on different machines that have
the same exact Gaussian 98 distribution so it is clearly the
installation that is bad.  I have attached the .log file generated and I
was hoping that someone can shed some light on my problem.  Like I said
this same version of Gaussian from the same .tar was installed by me
before on this machine and it does not run properly now.  Thank you in
advance for any help that anyone can give.  Have a good day.

 

Don

 

------------------------------------------------------------------------
---------------------------------------
Donald J. Keidel
University of California, Riverside
Department of Biochemistry and Molecular Biology
Riverside, CA 92521
phone:  (909) 787-5493
fax:  (909) 787-4434
dopetec@dslextreme.com
webpage: www.biochemistry.ucr.edu/gru/gradstudents/don_keidel/index.htm

 

 


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Hello all,



 



I have reinstalled Gaussian 98 rev.A.9 on the same =
computer
that it used to be installed on (and working before I formatted and =
changed the
hard drive – 5400 rpm hard drive) and tested the installation =
using the
test001.com file.  This same file runs on different machines that =
have the
same exact Gaussian 98 distribution so it is clearly the installation =
that is
bad.  I have attached the .log file generated and I was hoping that
someone can shed some light on my problem.  Like I said this same =
version
of Gaussian from the same .tar was installed by me before on this =
machine and
it does not run properly now.  Thank you in advance for any help =
that
anyone can give.  Have a good day.



 



Don



 



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

Donald J. Keidel

University of California, Riverside

Department of Biochemistry and Molecular Biology

Riverside, CA =
92521

phone:  (909) 787-5493

fax:  (909) 787-4434

dopetec@dslextreme.com

webpage: www.biochemistry.ucr.edu/gru/gradstudents/don_keidel/index.htm<=
/span>






 






 









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 Entering Gaussian System, Link 0=3Dg98=0A=
 Input=3Dtest001.com=0A=
 Output=3Dtest001.log=0A=
 Initial command:=0A=
 /usr/local/g98/l1.exe /usr/tmp/Gau-1356.inp -scrdir=3D/usr/tmp/=0A=
 Entering Link 1 =3D /usr/local/g98/l1.exe PID=3D      1357.=0A=
  =0A=
 Copyright (c) 1988,1990,1992,1993,1995,1998 Gaussian, Inc.=0A=
                  All Rights Reserved.=0A=
  =0A=
 This is part of the Gaussian(R) 98 program.  It is based on=0A=
 the Gaussian 94(TM) system (copyright 1995 Gaussian, Inc.),=0A=
 the Gaussian 92(TM) system (copyright 1992 Gaussian, Inc.),=0A=
 the Gaussian 90(TM) system (copyright 1990 Gaussian, Inc.),=0A=
 the Gaussian 88(TM) system (copyright 1988 Gaussian, Inc.),=0A=
 the Gaussian 86(TM) system (copyright 1986 Carnegie Mellon=0A=
 University), and the Gaussian 82(TM) system (copyright 1983=0A=
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 Cite this work as:=0A=
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 M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, =0A=
 M. A. Robb, J. R. Cheeseman, V. G. Zakrzewski, J. A. Montgomery, Jr., =0A=
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 A. D. Daniels, K. N. Kudin, M. C. Strain, O. Farkas, J. Tomasi, =0A=
 V. Barone, M. Cossi, R. Cammi, B. Mennucci, C. Pomelli, C. Adamo, =0A=
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 C. Y. Peng, A. Nanayakkara, M. Challacombe, P. M. W. Gill, =0A=
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 M. Head-Gordon, E. S. Replogle, and J. A. Pople, =0A=
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=0A=
 *********************************************=0A=
 Gaussian 98:  x86-Linux-G98RevA.9 19-Apr-2000=0A=
                  23-Apr-2003 =0A=
 *********************************************=0A=
 ------------------------------------------------=0A=
 #P TEST STO-3G COMPLEX pop=3Dfull scf=3Dconventional=0A=
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 Leave Link    1 at Wed Apr 23 14:12:00 2003, MaxMem=3D          0 cpu:  =
     0.4=0A=
 (Enter /usr/local/g98/l101.exe)=0A=
 ----------------------------------------------------------=0A=
 Gaussian Test Job 01 SINGLET DELTA STO-3G//STO-3G DIOXYGEN=0A=
 ----------------------------------------------------------=0A=
 Symbolic Z-matrix:=0A=
 Charge =3D  0 Multiplicity =3D 1=0A=
 O=0A=
 O                    1    R=0A=
       Variables:=0A=

------=_NextPart_000_0001_01C309BD.F4C31380--




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From: "Singh, Suresh" 
Subject: Deadline May 12th, 2003; Reminder: Novel database and knowledge
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> Dear Colleagues,
> This is a second call for papers for the symposium on Novel database and
> knowledge mining techniques at the Fall ACS national meeting to be held in
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> developed to mine chemical, informational, and knowledge databases. This
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> 
> All are invited to participate and submit abstracts for this session.
> Please use the OASYS to submit your abstract. You can access the CINF
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> 
> The deadline for submitting abstracts is May 12th, 2003. 
> 
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From chemistry-request@server.ccl.net Thu Apr 24 11:33:49 2003
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Message-ID: 
From: "WANG, YIXUAN " 
To: "'zjwu'" 
Cc: "'chemistry@ccl.net'" 
Subject: RE: Re: CPCM TS location
Date: Thu, 24 Apr 2003 11:33:45 -0400
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Dr. Wu,
 
You do not need wait for G03 to optimize TS in solution. If you
use qst2 algorithm  and define solvent field as usually, it is most likely
you could get TS in solution with G98. 
 
 
 
 
Yixuan  Wang
 
 
 

-----Original Message-----
From: zjwu [mailto:zjwu@ns.ciac.jl.cn]
Sent: Thursday, April 24, 2003 1:13 AM
To: help@gaussian.com
Cc: chemistry@ccl.net
Subject: CCL:Re: CPCM TS location



Dear Dr. Hess,

 

I mean the job failing because the structure is not the TS structure
anymore. The calculation may converge but goes to different geometry which I
did not want. I have tried to read force constants at cpcm calculation from
either gas phase frequency calculation or Onsager frequency calculation
(these frequencies are obtained based on the optimized geometry)
(calculation using Onsager model works well for the TS calculation). In
addition, I also tried opt=(ts,calcfc), but as you know, calcfc does not
exist for cpcm. It seems g03 is possible to calculate fc at cpcm level.

 

Hope I have made myself clear.

 

Thank you very much for your answer.

 

Best regards,

 

Zhijian Wu

 



  _____  




Dear Dr. Zhijian Wu,
    Is this job failing because it runs out of optimization cycles? I'd 
need to know more details about what is going wrong before I make 
detailed suggestions, but one possible way to improve this calculation 
is to calculate the force constants in the solution phase, then use 
these force constants to start the transition state search. Usually the 
gas-phase Hessian is a good enough approximation, but in some cases 
where the gas-phase and solution-phase potential energy surfaces are 
different enough, explicitly calculating the second derivatives in the 
solution phase can be helpful. Incidentally, if you are using G98, the 
CPCM second derivatives will be performed by numerical differentiation 
of the analytic gradients and if you are using G03, the second 
derivatives will be calculated analytically.
 
Regards,
Jim Hess
 
++++++++++++++++++++++++++
James Hess, Ph.D.
Customer Support Scientist
Gaussian, Inc.
e-mail: help@gaussian.com
++++++++++++++++++++++++++
 
 
On Tuesday, April 22, 2003, at 08:29 PM, zjwu wrote:
 
>>  Dear members,
>> 
>>  ?/DIV> 
>> 
>>  I am trying to locate the transition state using cpcm model. The 
>>  initial structure is from gas phase optimized transition structure 
>>  (with correct vibrational mode). The optimization at cpcm level fails 
>>  by the following keywords
>> 
>>  ?/DIV> 
>> 
>>  #b3lyp/6-31g(d,p) opt=(ts, readfc, noeigen) scrf=(cpcm,solvent=water)
>> 
>>  ?/DIV> 
>> 
>>  Do anybody has experience in cpcm transition structure calculation?
>> 
>>  ?/DIV> 
>> 
>>  Thanks a lot.
>> 
>>  ?/DIV> 
>> 
>>  Best regards,
>> 
>>  ?/DIV> 
>> 
>>  Zhijian Wu
>> 
Dear Dr. Zhijian Wu,
 
   Is this job failing because it runs out of optimization cycles? I'd
need to know more details about what is going wrong before I make
detailed suggestions, but one possible way to improve this calculation
is to calculate the force constants in the solution phase, then use
these force constants to start the transition state search. Usually
the gas-phase Hessian is a good enough approximation, but in some
cases where the gas-phase and solution-phase potential energy surfaces
are different enough, explicitly calculating the second derivatives in
the solution phase can be helpful. Incidentally, if you are using G98,
the CPCM second derivatives will be performed by numerical
differentiation of the analytic gradients and if you are using G03,
the second derivatives will be calculated analytically.
 
 
Regards,
 
Jim Hess
 
 
++++++++++++++++++++++++++
 
James Hess, Ph.D.          
 
Customer Support Scientist
 
Gaussian, Inc.
 
e-mail: help@gaussian.com
 
++++++++++++++++++++++++++
 
 
 
On Tuesday, April 22, 2003, at 08:29 PM, zjwu wrote:
 
 
<< excerpt> Dear members,
 
 
?/DIV> 
 
 
I am trying to locate the transition state using cpcm model. The
initial structure is from gas phase optimized transition structure
(with correct vibrational mode). The optimization at cpcm level fails
by the following keywords
 
 
?/DIV> 
 
 
#b3lyp/6-31g(d,p) opt=(ts, readfc, noeigen) scrf=(cpcm,solvent=water)
 
 
?/DIV> 
 
 
Do anybody has experience in cpcm transition structure calculation?
 
 
?/DIV> 
 
 
Thanks a lot.
 
 
?/DIV> 
 
 
Best regards,
 
 
?/DIV> 
 
 
Zhijian Wu
 
 
<< /excerpt> 
  _____  



------_=_NextPart_001_01C30A76.E45E9B90
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	charset="gb2312"
Content-Transfer-Encoding: quoted-printable









Dr.=20
Wu,


 


You do=20
not need wait for G03 to optimize TS in solution. If =
you


use qst2 algorithm  and define solvent field as =
usually, it is=20
most likely


you=20
could get TS in solution with G98. 


 


 


 


 


Yixuan  Wang


 


 


 



  
-----Original Message-----
From: zjwu=20
  [mailto:zjwu@ns.ciac.jl.cn]
Sent: Thursday, April 24, 2003 =
1:13=20
  AM
To: help@gaussian.com
Cc:=20
  chemistry@ccl.net
Subject: CCL:Re: CPCM TS=20
  location


  
Dear Dr. Hess,

  
 

  
I mean the job failing because the structure is not the TS =
structure=20
  anymore. The calculation may converge but goes to different geometry =
which I=20
  did not want. I have tried to read force constants at cpcm =
calculation from=20
  either gas phase frequency calculation or Onsager frequency =
calculation (these=20
  frequencies are obtained based on the optimized geometry) =
(calculation using=20
  Onsager model works well for the TS calculation). In addition, I =
also=20
  tried opt=3D(ts,calcfc), but as you know, calcfc does not exist=20
  for cpcm. It seems g03 is possible to calculate fc at cpcm=20
level.

  
 

  
Hope I have made myself clear.

  
 

  
Thank you very much for your answer.

  
 

  
Best regards,

  
 

  
Zhijian Wu

  
 

  

  


  

  
Dear Dr. Zhijian Wu,

  =

    Is this job failing bec=
ause it runs out of optimization cycles?&n=
bsp;I'd 

  =

need to know more details about what&=
nbsp;is going wrong before I make 

  =

detailed suggestions, but one possible way=
 to improve this calculation 

  
is to calculate the force constants =
;in the solution phase, then use 

  =

these force constants to start the tr=
ansition state search. Usually the 

  =

gas-phase Hessian is a good enough ap=
proximation, but in some cases 

  =

where the gas-phase and solution-phase pot=
ential energy surfaces are 

  =

different enough, explicitly calculating the&nb=
sp;second derivatives in the 

  =

solution phase can be helpful. Incidentall=
y, if you are using G98, the 

  =

CPCM second derivatives will be performed&=
nbsp;by numerical differentiation 

  =

of the analytic gradients and if you&=
nbsp;are using G03, the second 

  =

derivatives will be calculated analytically.
  
 

  
Regards,

  
Jim Hess

  
 

  
++++++++++++++++++++++++++

  
James Hess, Ph.D.

  
Customer Support Scientist

  
Gaussian, Inc.

  
e-mail: help@gaussian.com

  
++++++++++++++++++++++++++

  
 

  
 

  =

On Tuesday, April 22, 2003, at 08:29&=
nbsp;PM, zjwu wrote:

  
 

  
>>  Dear members,

  
>> 

  
>>  ?/DIV>=20
  
>> 

  
>>=20
  =
 I am trying to locate the transition=
 state using cpcm model. The 

  
>>=20
  =
 initial structure is from gas phase =
optimized transition structure 

  
>>=20
  =
 (with correct vibrational mode). The opti=
mization at cpcm level fails 

  
>>  by the following keywords

  
>> 

  
>>  ?/DIV>=20
  
>> 

  
>>=20
  =
 #b3lyp/6-31g(d,p) opt=3D(ts, readfc, noeigen) =
scrf=3D(cpcm,solvent=3Dwater)

  
>> 

  
>>  ?/DIV>=20
  
>> 

  
>>=20
  =
 Do anybody has experience in cpcm tr=
ansition structure calculation?

  
>> 

  
>>  ?/DIV>=20
  
>> 

  
>>  Thanks a lot.

  
>> 

  
>>  ?/DIV>=20
  
>> 

  
>>  Best regards,

  
>> 

  
>>  ?/DIV>=20
  
>> 

  
>>  Zhijian Wu

  
>> 

  
Dear Dr. Zhijian Wu,

  
 

  =

   Is this job failing because&n=
bsp;it runs out of optimization cycles? I'=
d

  =

need to know more details about what&=
nbsp;is going wrong before I make

  =

detailed suggestions, but one possible way=
 to improve this calculation

  =

is to calculate the force constants i=
n the solution phase, then use

  
these force constants to start the =
transition state search. Usually

  =

the gas-phase Hessian is a good enoug=
h approximation, but in some

  =

cases where the gas-phase and solution-pha=
se potential energy surfaces

  =

are different enough, explicitly calculating&nb=
sp;the second derivatives in

  =

the solution phase can be helpful. In=
cidentally, if you are using G98,

  =

the CPCM second derivatives will be p=
erformed by numerical

  =

differentiation of the analytic gradients =
and if you are using G03,

  =

the second derivatives will be calculated&=
nbsp;analytically.

  
 

  
 

  
Regards,

  
 

  
Jim Hess

  
 

  
 

  
++++++++++++++++++++++++++

  
 

  =

James Hess, Ph.D.      &nbs=
p;   

  
 

  
Customer Support Scientist

  
 

  
Gaussian, Inc.

  
 

  
e-mail: help@gaussian.com

  
 

  
++++++++++++++++++++++++++

  
 

  
 

  
 

  =

On Tuesday, April 22, 2003, at 08:29&=
nbsp;PM, zjwu wrote:

  
 

  
 

  
<< excerpt> Dear members,

  
 

  
 

  
?/DIV>=20
  
 

  
 

  =

I am trying to locate the transition&=
nbsp;state using cpcm model. The

  =

initial structure is from gas phase o=
ptimized transition structure

  =

(with correct vibrational mode). The optim=
ization at cpcm level fails

  
by the following keywords

  
 

  
 

  
?/DIV>=20
  
 

  
 

  =

#b3lyp/6-31g(d,p) opt=3D(ts, readfc, noeigen) s=
crf=3D(cpcm,solvent=3Dwater)

  
 

  
 

  
?/DIV>=20
  
 

  
 

  =

Do anybody has experience in cpcm tra=
nsition structure calculation?

  
 

  
 

  
?/DIV>=20
  
 

  
 

  
Thanks a lot.

  
 

  
 

  
?/DIV>=20
  
 

  
 

  
Best regards,

  
 

  
 

  
?/DIV>=20
  
 

  
 

  
Zhijian Wu

  
 

  
 

  
<< /excerpt> 

  

  =

=



------_=_NextPart_001_01C30A76.E45E9B90--


From chemistry-request@server.ccl.net Thu Apr 24 10:48:55 2003
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From: elewars 
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To: Peter Gannett , chemistry@ccl.net
Subject: Re: CCL:Chemistry and architecture relationships
References: 
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2003 April 24

Hello,

Don't forget pyramidane (the pyramids are the only architectural wonder of the ancient world still standing; may the molecule be as stable!

THEOCHEM, 1998, _423_, 173
THEOCHEM, 2000, _507_, 165

E. Lewars
====

Peter Gannett wrote:

> Miquel:
>
> Sounds like a tough audience.  Here are a few that come to mind and might help.
>
> Hydrocarbons:  Tetrahedran, housane, basketane, cubane (just search on the names to get structures for but you can get a good idea of what they look like from their names).  There are also the catenanes (two rings, one passing through the other).
>
> Others come to mind but need a bit of imagination, for example, DNA looks like a spiral staircase.
>
> Hope this helps.
>
> Pete Gannett
>
> >>> Miquel Solà  04/19/03 10:14AM >>>
>
> Dear CCLers,
>
> I have to give a talk to graduate students in Architecture on tools used
> for chemists to
> display molecular properties. I would like to start the introduction
> with a reference to
> relationships between chemistry and architecture. I know only one clear
> example
> of this relation which is the C60 molecule called buckminsterfullerene
> for its similarity
> with the geodesic domes made by the architect Richard Buckminster
> Fuller. Do you know
> other examples? I will post a summary if there is interest. Thanks in
> advance for your answers.
>
> Best regards,
>
> Miquel
>
>  -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
>  Miquel Solà
>  Institut de Química Computacional
>  Universitat de Girona
>  Campus Montilivi
>  17071 Girona, CATALONIA (Spain)
>  Phone +34.972.41.89.12
>  Cellular-Phone:  +34.626.163.580
>  FAX   +34.972.41.83.56
>  World Wide Web: http://iqc.udg.es/~miquel/mike.html
>  e-mail: miquel.sola@udg.es
>  -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
>
> -= This is automatically added to each message by mailing script =-
> CHEMISTRY@ccl.net -- To Everybody  | CHEMISTRY-REQUEST@ccl.net -- To Admins
> Ftp: ftp.ccl.net  |  WWW: http://www.ccl.net/chemistry/   | Jan: jkl@ccl.net



From chemistry-request@server.ccl.net Thu Apr 24 08:57:53 2003
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From: "Frank   Marchese" 
Reply-To: 
X-Sender: 
To: 
Subject: Molecular Architecture
X-Mailer: 

Hi All,

Architects and structural chemists have similar design goals. Below are
a few architecture concepts that can be mapped to molecules.

1. Architecture defines space. 
So do molecules. For example, cage compounds, zeolites, many 
proteins define spaces for other molecules to inhabit. 
(keywords: host-guest compounds, cages, cryptands, protein active site) 

2. Form follows function. 
For example, the "shapes" of proteins have evoled to perform a specific
function.

3. Architectural orders. 
There is a systematic way in which atoms are combined to create spatial
structure. Models such as VSEPR are easy heuristic models to look at this. Correlations may be made with Palladian motifs. Mitchell's book "The Logic of Architecture" talks about "a Palladian grammar" that is used to understand how Palladio designed his buildings. The periodic table and rules of chemical combination are a more complex 3D grammar.

As another example... Proteins are built from a set of architectural "motifs" (e.g. "greek key"). A good place to look is "Introduction to Protein Structure" by Carl Branden and John Tooze.

Finally, molecules crystallize in regular patterns, very much like "wall paper" patterns. Books on symmetry and crystallography are good places to look for info.

4. Inorganic vs organic architecture. 
Inorganic substances have highly regular structures (e.g. salt (NaCl)). But 
most organic molecules are less-so. There is a whole class of molecules
called "dendritic molecules" that have branching patterns much like 
trees or bushes.

5. Positive vs Negative space. 
The Seagram building in NYC is my favorite example of this. Mies van der Rohe's 
monolithic structure defines a complmentary rectangular volume.  Many atomic
arrangements create these types of  spatial relationships. For example, the packing
arrangement of Cl- ions in the NaCl lattice defines spaces for the smaller Na+ ions
to occupy.


Enough for now.

Regards
Frank

Dr. Francis T. Marchese
Professor
Dept. of Computer Science
Pace University
163 William Street, 2nd Floor
NY, NY 10038

and

Director
Center for Advanced Media
http://csis.pace.edu/~cam

and 

Director
Pace Digital Gallery
http://www.pace.edu/DigitalGallery




 

_______________________________________________________________________
Sent via Pace University's WebMail system at fsmail.pace.edu


 
                   


From chemistry-request@server.ccl.net Thu Apr 24 10:18:21 2003
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Date: Thu, 24 Apr 2003 10:18:17 -0400
Subject: Re: CCL:Chemistry and architecture relationships
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To: "Shobe, Dave" 
From: Richard Gillilan 
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I once gave an invited lecture on molecular graphics at a conference on  
oil and
gas discovery. They invited a variety of speakers from different fields  
to get
a perspective on visualization methods and technology. One of the  
things molecular
graphics has to offer is the ways in which various simplified  
representations are
used to bring out different aspects of a more complex data set. Ribbon  
representation
for example, removes the complexity of sidechains and focuses on the  
underlying architectural structure of the protein. Molecular surface  
focuses on the shape and
surface form without regard to interior. Biochemists may have some of  
the most complex
geometric data to deal with in any field. Architects are only recently  
getting into
3D (stereo and VR) display technology, while chemists have used it for  
decades.
Although architects are quite good at photorealism now (more so than  
chemists I think),
it always surprises me that so little use is made of depth-cuing (fade  
to black with
distance) and stereo in geometric modeling programs (geometric modelers  
in
film/animation fall in this category too). Could be that man-made  
structures are
(have been) easier to visualize with simple orthographic  
(front/back/side)
projections than natural 3D objects. Molecular building programs in  
chemistry & crystallography contain integrated physical simulations  
(structure
minimization for example).  The analogy would be designing a building  
using
real-time load-bearing simulations or something of that type.
If you are interested, I could probably
dig up some old slides.

Richard Gillilan
MacCHESS, Cornell


On Monday, April 21, 2003, at 09:23 AM, Shobe, Dave wrote:

> You might want to look at "supramolecular" chemistry, where molecules  
> are used as "building blocks" to make more complicated structures.   
> Typically these are held together by hydrogen bonds or similar  
> interactions.
>  
> There are also articles on molecular versions of the construction  
> toys, "Tinkertoys" and "Meccano", perhaps others.  (These are  
> analogies used by the authors of the papers, but do are not meant  
> to imply any connection to the companies that manufacture these toys  
> or own the trademarks thereto).  These are typically rigid molecules  
> which react, forming covalently bonded structures.
>  
> Hope this helps,
>
> --David Shobe
> Süd-Chemie Inc.
> phone (502) 634-7409
> fax     (502) 634-7724
> email  dshobe@sud-chemieinc.com
>
> Don't bother flaming me: I'm behind a firewall.
>
>  
>
> -----Original Message-----
> From: Miquel Solà [mailto:miquel.sola@udg.es]
> Sent: Saturday, April 19, 2003 10:14 AM
> To: chemistry@ccl.net
> Subject: CCL:Chemistry and architecture relationships
>
>
> Dear CCLers,
>
> I have to give a talk to graduate students in Architecture on tools  
> used for chemists to
> display molecular properties. I would like to start the introduction  
> with a reference to
> relationships between chemistry and architecture. I know only one  
> clear example
> of this relation which is the C60 molecule called buckminsterfullerene  
> for its similarity
> with the geodesic domes made by the architect Richard Buckminster  
> Fuller. Do you know
> other examples? I will post a summary if there is interest. Thanks in  
> advance for your answers.
>
> Best regards,
>
> Miquel
>
>   
> -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
> *-*-
>  Miquel Solà
>  Institut de Química Computacional
>  Universitat de Girona
>  Campus Montilivi
>  17071 Girona, CATALONIA (Spain)
>  Phone +34.972.41.89.12
>  Cellular-Phone:  +34.626.163.580
>  FAX   +34.972.41.83.56
>  World Wide Web: http://iqc.udg.es/~miquel/mike.html
>  e-mail: miquel.sola@udg.es
>   
> -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
> *-*-
>



From chemistry-request@server.ccl.net Thu Apr 24 03:24:59 2003
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From: 
Subject: H-bond constraint file in QXP (FLO)
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Dear all,

For those who are familiar with FLO, I was wondering
if there is a way one can define a H-bond constraint
file between an atom in the ligand and an atom in the
protein/enzyme. If there is a way once can do it then
how does one go about defining that constraint file.

Thanks.

Yogesh

=====

Yogesh Sabnis, PhD 

Box 574, 

Avd Org. Farm. Kemi, 

BMC, Husargatan 3, 

Uppsala - 75123 

Sweden


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From chemistry-request@server.ccl.net Thu Apr 24 15:37:31 2003
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Date: Thu, 24 Apr 2003 20:37:30 +0100 (BST)
From: Andreas Bender 
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Subject: CCL:Grid energy minimization
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Sender: Andreas Bender 

Hi Jay,

It's related to the problem of aligning two molecules on a 3D grid for
example when using Carbo or Hodgkin similarity indices (where you try to
maximize the integral over the product of two functions that depend
on relative molecular orientation) - here the problem is not in the
minimization algorithm itself but rather in the representation at
discrete grid values.

In this case, the problem was "solved" using Gaussian representations of
molecules (e.g. Good AC, Hodgkin EE and Richards WG, JCICS 1992 (32)
188-191). The difference between the approaches is illustrated by the
problems you run into when you superimpose two _identical_ molecules using
values at grid points and a downhill (steepest gradient) optimization -
the superposition looks rather awful (I can't recall the reference right
now but can look it up if you are interested), Gaussian representations
are much more well-behaved for this task (here especially because of the
integrations one performs).

The point why it could be interesting for you: Although your task seems to
be different, you still have a function that is defined at grid
points and you wand to optimize it. Maybe you can transform your
representation of discrete points and perform the minimization in some
transformed space.

Best wishes & Good luck,
Andreas

____________________________________________

Andreas Kieron Patrick Bender
http://www.andreasbender.de

E-mail1: ab454@cam.ac.uk
E-mail2: Andreas.Bender@Alumni.TU-Berlin.DE
ICQ: 166 835 816

PhD student at Cambridge University /
Unilever Centre for Molecular Informatics
___________________________________________


On Tue, 22 Apr 2003, Jay Banks wrote:

> Hi --
>
> Does anyone have experience with minimizing potential energy functions
> defined at (or interpolated between) points on a 3-dimensional grid?
> The minimizer I've been using has occasional problems, which I think are
> associated with discontinuities at the edges of grid boxes, etc.
>
> I know that the "downhill simplex" algorithm (Nelder & Mead, Computer
> J. 7: 308 (1965)) can be useful for discontinuous functions (and/or
> discontinuous derivatives), but I doubt that it is practical for my
> purposes given the high dimensionality of my problem.  So I'd be
> interested in hearing about modifications of other "standard" methods,
> as well as anything "new" that anyone has come up with.
>
>
> Sincerely,
> Jay Banks
>
> (banks "at" schrodinger "dot" com)
>
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