From chemistry-request@ccl.net Thu Jun 26 17:34:02 2003 Received: from MMSSERVER.chla.usc.edu (chl179129.usc.edu [128.125.179.129]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5QLY15u006483 for ; Thu, 26 Jun 2003 17:34:02 -0400 Received: from 10.3.1.165 by MMSSERVER.chla.usc.edu with ESMTP (CHLA SMTP Relay (MMS v5.5.2)); Thu, 26 Jun 2003 14:35:27 -0700 Received: by NTSMTP01 with Internet Mail Service (5.5.2653.19) id ; Thu, 26 Jun 2003 14:33:19 -0700 Message-ID: <73564B8DE398D61180500008C75D7E49438A3E@NTMAIL03> From: "Pandey, Jaya" To: "'chemistry)at(ccl.net'" Subject: peptidomimetics Date: Thu, 26 Jun 2003 14:33:17 -0700 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) X-WSS-ID: 12E5B895189187-01-01 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 7bit Hi All, Can someone send me tips on designing inhibitor peptides to a target protein. Thanks, Jaya -----Original Message----- From: Chandra Verma [mailto:chandra)at(ysbl.york.ac.uk] Sent: Monday, June 23, 2003 3:52 AM To: Computational Chemistry List Subject: CCL:Help Hi I am trying to get a set of charges (Mulliken analysis) on a system that has two Nickel atoms that are coordinated to various residues in a a protein, using GAMESS. I would appreciate any help on the kinds of basis sets that ought to be used.... thanks chandra -= This is automatically added to each message by mailing script =- To send e-mail to subscribers of CCL put the string CCL: on your Subject: line and send your message to: CHEMISTRY)at(ccl.net Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST)at(ccl.net HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs If your mail is bouncing from CCL.NET domain send it to the maintainer: Jan Labanowski, jkl)at(ccl.net (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Thu Jun 26 14:28:43 2003 Received: from linus.imcm.cas.cz (Linus.imcm.cas.cz [147.231.77.250]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5QISg5u002573 for ; Thu, 26 Jun 2003 14:28:43 -0400 Received: from localhost (ccl@localhost) by linus.imcm.cas.cz (8.9.3/8.9.3) with ESMTP id UAA27741; Thu, 26 Jun 2003 20:28:57 +0200 Date: Thu, 26 Jun 2003 20:28:56 +0200 (CEST) From: Petr Toman To: Dai Bing cc: CHEMISTRY)at(ccl.net Subject: Re: CCL:the ground state calculation with g98 In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, Do you use a spin restricted or unrestricted method? If restricted, try the unrestricted one and use Guess=Alter only for the exchange of beta HOMO and LUMO, although you expect a closed shell. I had a similar problem with some cations of Metal-phthalocyanines (you can see P. Toman, S. Nespurek, K. Yakushi: J. Porphyrins Phthalocyanines 2002; 6: 556-562) Btw. what molecule do you calculate? Yours, Petr Toman On Fri, 13 Jun 2003, Dai Bing wrote: > Dear CCLers, > A simple Opt calculation with g98, HOMO and LUMO are the > same symmetry, such as PI. But the energy of LUMO is lower than > the one of HOMO, what's the problem? and how to resolve? > The following two methods don't work. :( > 1. Stable=opt. > 2. change the symmetry of the molecule, HOMO and LUMO > change to A1 and B1, then use guess=alter. > > Can someone help me? Thanks. > > = = = = = = = = = = = = = = = = = = = = > > =============== > Bing Dai, > Ph.D. Candidate, > Laboratory of Bond Selective Chemistry, > University of Science and Technology of China, > Chinese Academy of Sciences. > Hefei, Anhui, 230026, > People's Republic of China, > Tel.: 86-551-3603418,3603748,3601084 > Fax.: 86-551-3602969 > Http://www.bsc.ustc.edu.cn/~bdai > E-mail: bdai)at(mail.ustc.edu.cn > =============== > > > > -= This is automatically added to each message by mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY)at(ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST)at(ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jkl)at(ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > From chemistry-request@ccl.net Wed Jun 25 04:58:33 2003 Received: from century.fen.bilkent.edu.tr (century.fen.bilkent.edu.tr [139.179.97.100]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5P8wS5u015055 for ; Wed, 25 Jun 2003 04:58:32 -0400 Received: from fen.bilkent.edu.tr (fenII-124.fen.bilkent.edu.tr [139.179.97.239]) by century.fen.bilkent.edu.tr (8.12.8/8.12.8) with ESMTP id h5P8qNQn007279 for ; Wed, 25 Jun 2003 11:52:24 +0300 (EET DST) Message-ID: <3EF96541.5080108^at^fen.bilkent.edu.tr> Date: Wed, 25 Jun 2003 12:02:57 +0300 From: Ulrike Salzner Organization: Bilkent University User-Agent: Mozilla/5.0 (Windows; U; Win98; en-US; rv:1.0.2) Gecko/20030208 Netscape/7.02 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry Subject: CCL: TDHF Content-Type: multipart/alternative; boundary="------------080406010706030201000105" --------------080406010706030201000105 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Many thanks to Stefan Grimme, Artem Masumov, and Doug Fox. I asked whether it is possible to calculate and optimize the ground state of a system with TDHF. The answer is no. Like CIS, TDHF does not provide a correction to the ground state energy. More important I was warned that the TDHF geometry optimization for excited states in G98 is an approximation and should not be used. The option has been removed in G03. One comment of mine to the statement that TDDFT is superior to TDHF: I am aware that TDDFT is quite successful in general. Unfortunately, the only excited state that is currently of interest to me (the 1Bu excited state of polyenes) is not well reproduced, especially with increasing size and conjugation length, which is exactly what I need to investigate. TDHF, in contrast, gives numbers similar to CASMP2. Therefore, it is bad news indeed that the geometries can not be optimized at this level of theory. The original question and the answers follow below: Hello, > the time-dependent Hartree-Fock method is described as a method for > calculating excited states. I would like to know whether one can also > optimize the ground state including correlation with TDHF. In other > words, if I use the keywords "fopt" and "nroot=0" in Gaussian what am I > calculating? I know that CIS does not make a correction to the ground > state because of Brillouin's theorem but I am not sure what TDHF > includes exactly. The reason why I am considering this is that I would > like to compare the excitet state and the ground state geometries on > equal footing. Would it be better to compare the excited state TDHF > geometry to the HF ground state geometry? > Thanks in advance, > Ulrike Salzner Dear Ulrike, in fact TDHF is not defined for the ground state but there is a close analogy between CIS and TDHF (expanded in singles only, CIS equations can be derived from the non-Hermitian TDHF problem by neglecting the so-called B-matrix). >From that I would argue that the ground state analogue of TDHF is just HF. Regards Stefan _________________________________________________________ Prof. Dr. Stefan Grimme Organisch-Chemisches Institut (Abt. Theoretische Chemie) Westfaelische Wilhelms-Universitaet, Corrensstrasse 40 D-48149 Muenster, Tel (+49)-251-83 36512/33241/36515(Fax) Ulrike, Just like CIS, TDHF does not improve the ground state. So correct comparison would be TDHF optimized excited state and HF optimized ground state. In fact, TDHF only differs from CIS in that it has nonzero V-O block in hamiltonian (and thus, in transition density) matrix. In g98 this block is missing from the routine evaluating gradients, so excited state optimization with analytical gradients gives incorrect (approximate) results. That is why in g03 this option is blocked. In Turbomol TDHF opt. is coded fine. To optimize the excited state at TDHF level you need to do Opt=Numer, which is much slower. Please keep in mind that TDHF is inferior to TDDFT at the same computational cost. Hope this helps, Artem ________________________________________________________ __ ___________ Artem.Masunov^at^LANL.gov / \ / __ __ \ www.t12.lanl.gov/home/amasunov / \/\ \ \ \ \ \ 505.665.2635, Fax:505.665.3909 / /\ \ \ \ \ \ \ \ Theoretical Division, MS B268 / ____ \ \ \ \ \ \ \ Los Alamos National Lab /__/\ _/\ _\ \ _\ \ _\ \ _\ Los Alamos NM 87545 \ _\/ \/__/\ __/\ __/\ __/ ____________________________ Dr. Salzner, G98/03 does not have gradients implement analytic gradients for TDHF or TDDFT so optimizations need to be performed with only energy values OPT=(EF,EnOnly) and a symbolic Z-matrix. But it can be done for medium to small systems. Or at least a few degrees of freedom. The TDHF and CIS methods both use the HF solution as the reference and neither of them improve on the ground state description. In the sense that neither the Excited state or the Ground state is really correlated it has been our experience that structures in CIS are similar in quality to HF although often a slightly larger basis is needed. To go beyond this you might want to consider SACCI which is in G03 or CASSCF, both of which can include correlation, dynamic vs. static, and treat ground and excited state on a equal footing. --------------080406010706030201000105 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Many thanks to Stefan Grimme, Artem Masumov, and Doug Fox.

I asked whether it is possible to calculate and optimize the ground state of a system with TDHF. The answer is no. Like CIS, TDHF does not provide a correction to the ground state energy. More important I was warned that the TDHF geometry optimization for excited states in G98 is an approximation and should not be used. The option has been removed in G03.

One comment of mine to the statement that TDDFT is superior to TDHF: I am aware that TDDFT is quite successful in general. Unfortunately, the only excited state that is currently of interest to me (the 1Bu excited state of polyenes) is not well reproduced, especially with increasing size and conjugation length, which is exactly what I need to investigate. TDHF, in contrast, gives numbers similar to CASMP2. Therefore, it is bad news indeed that the geometries can not be optimized at this level of theory.

The original question and the answers follow below:

Hello,
> the time-dependent Hartree-Fock method is described as a method for
> calculating excited states. I would like to know whether one can also
> optimize the ground state including correlation with TDHF. In other
> words, if I use the keywords "fopt" and "nroot=0" in Gaussian what am I
> calculating? I know that CIS does not make a correction to the ground
> state because of Brillouin's theorem but I am not sure what TDHF
> includes exactly.  The reason why I am considering this is that I would
> like to compare the excitet state and the ground state geometries on
> equal footing. Would it be better to compare the excited state TDHF
> geometry to the HF ground state geometry?
> Thanks in advance,
> Ulrike Salzner


Dear Ulrike, 
in fact TDHF is not defined for the ground state but there is a close
analogy between CIS and TDHF (expanded in singles only,
CIS equations can be derived from the non-Hermitian TDHF
problem by neglecting the so-called B-matrix). 
>From that I would argue that the ground state analogue of TDHF is just HF.
Regards 
Stefan
_________________________________________________________
Prof. Dr. Stefan Grimme
Organisch-Chemisches Institut (Abt. Theoretische Chemie)
Westfaelische Wilhelms-Universitaet, Corrensstrasse 40
D-48149 Muenster, Tel (+49)-251-83 36512/33241/36515(Fax)

Ulrike,

Just like CIS, TDHF does not improve the ground state.
So correct comparison would be TDHF optimized excited state and HF
optimized ground state.

In fact, TDHF only differs from CIS in that it has nonzero V-O block in
hamiltonian (and thus, in transition density) matrix.

In g98 this block is missing from the routine evaluating gradients, so
excited state optimization with analytical gradients gives incorrect
(approximate) results. That is why in g03 this option is blocked. In
Turbomol TDHF opt. is coded fine.

To optimize the excited state at TDHF level you need to do Opt=Numer,
which is much slower.

Please keep in mind that TDHF is inferior to TDDFT at the same
computational cost.

Hope this helps,
Artem

________________________________________________________
     __    ___________        Artem.Masunov^at^LANL.gov
    /  \  /  __   __  \   www.t12.lanl.gov/home/amasunov
   /    \/\  \ \  \ \  \  505.665.2635, Fax:505.665.3909
  /  /\  \ \  \ \  \ \  \  Theoretical Division, MS B268
 /  ____  \ \  \ \  \ \  \    Los Alamos National Lab
/__/\ _/\ _\ \ _\ \ _\ \ _\     Los Alamos NM 87545
\ _\/  \/__/\ __/\ __/\ __/ ____________________________


  

Dr. Salzner,

   G98/03 does not have gradients implement analytic gradients for
TDHF or TDDFT so optimizations need to be performed with only
energy values OPT=(EF,EnOnly) and a symbolic Z-matrix.  But it
can be done for medium to small systems.  Or at least a few degrees
of freedom.

   The TDHF and CIS methods both use the HF solution as the reference
and neither of them improve on the ground state description.

   In the sense that neither the Excited state or the Ground state
is really correlated it has been our experience that structures in
CIS are similar in quality to HF although often a slightly larger basis    
is needed.    To go beyond this you might want to consider SACCI
which is in G03 or CASSCF, both of which can include correlation,
dynamic vs. static, and treat ground and excited state on a equal
footing.

--------------080406010706030201000105-- From chemistry-request@ccl.net Wed Jun 25 12:51:37 2003 Received: from klingon.uab.es (klingon.uab.es [158.109.14.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5PGpa5u028446 for ; Wed, 25 Jun 2003 12:51:37 -0400 Received: from olivier by klingon.uab.es with local (Exim 3.36 #1 (Debian)) id 19VDK7-0007mf-00; Wed, 25 Jun 2003 18:40:43 +0200 To: chemistry..at..ccl.net Subject: Triple Zeta Sn Cc: lougras..at..yahoo.fr Message-Id: From: olivier maresca Date: Wed, 25 Jun 2003 18:40:43 +0200 Him, does anybody know if there are any triple zeta with pseudo (i am currently using LanL2DZ) basis sets for the Sn. Best regards olivier From chemistry-request@ccl.net Tue Jun 24 08:45:39 2003 Received: from mailhub.usp.br (serv1.uspnet.usp.br [143.107.253.61]) by server.ccl.net (8.12.8/8.12.8) with SMTP id h5OCjc5u025322 for ; Tue, 24 Jun 2003 08:45:39 -0400 Received: (qmail 2347 invoked from network); 24 Jun 2003 12:35:43 -0000 Received: from unknown (HELO notebook) (143.107.221.197) by mailhub.usp.br with SMTP; 24 Jun 2003 12:35:42 -0000 Message-ID: <000a01c33a4c$8d5e5140$c5dd6b8f[at]ffclrp.usp.br> Reply-To: "Sergio Emanuel Galembeck" From: "Sergio Emanuel Galembeck" To: Subject: CCL: AIM critical points analysis Date: Tue, 24 Jun 2003 09:31:00 -0300 Organization: =?iso-8859-1?Q?Universidade_de_S=E3o_Paulo?= MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1158 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 Dear colleagues, I am trying to analyse the critical points for a molecule, but I didn't found the exact meaning of some variables as L(r), Vnuc(r) and V(r). Thank you very much in advance, Sergio Galembeck ============================================================== Sergio Emanuel Galembeck Laboratorio de Modelagem Molecular Departamento de Quimica Faculdade de Filosofia, Ciencias e Letras de Ribeirao Preto Universidade de Sao Paulo ============================================================== From chemistry-request@ccl.net Fri Jun 27 12:08:09 2003 Received: from sccrmhc11.attbi.com (sccrmhc11.attbi.com [204.127.202.55]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5RG895u026104 for ; Fri, 27 Jun 2003 12:08:09 -0400 Received: from C1353359A (12-207-202-98.client.attbi.com[12.207.202.98](untrusted sender)) by attbi.com (sccrmhc11) with SMTP id <2003062716080801100dkrute>; Fri, 27 Jun 2003 16:08:08 +0000 Reply-To: From: "Mark Thompson" To: Subject: CCL: ArgusLab site licences Date: Fri, 27 Jun 2003 09:02:33 -0700 Message-ID: <000001c33cc5$8527d570$0300a8c0(at)attbi.com> MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) Importance: Normal In-Reply-To: X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 (Apologies for the non-technical bandwith) We would like to announce that site licenses are now available for ArgusLab. To learn more please click on the "Site License" link from our website: http://www.planaria-software.com/ ================================= Mark Thompson, Ph.D. Planaria Software PO Box 55207 Seattle, WA 98155 FAX: 206-440-3305 ArgusLab is available at: http://www.arguslab.com ================================= From chemistry-request@ccl.net Wed Jun 25 13:41:54 2003 Received: from mailhub.usp.br (serv1.uspnet.usp.br [143.107.253.61]) by server.ccl.net (8.12.8/8.12.8) with SMTP id h5PHfe5u029617 for ; Wed, 25 Jun 2003 13:41:41 -0400 Received: (qmail 11837 invoked from network); 25 Jun 2003 17:41:16 -0000 Received: from unknown (HELO notebook) (143.107.221.197) by mailhub.usp.br with SMTP; 25 Jun 2003 17:41:16 -0000 Message-ID: <004501c33b40$656b9180$c5dd6b8f_at_ffclrp.usp.br> Reply-To: "Sergio Emanuel Galembeck" From: "Sergio Emanuel Galembeck" To: Subject: CCL: program for docking of small molecules Date: Wed, 25 Jun 2003 14:37:05 -0300 Organization: =?iso-8859-1?Q?Universidade_de_S=E3o_Paulo?= MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1158 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 Dear colleagues, I am studying the interaction between two large aromatic dye molecules and I need to locate the conformation of minimum energy of interaction. Is there any software that can do a docking for small molecules? Thank you very much, Sergio From chemistry-request@ccl.net Thu Jun 26 16:45:58 2003 Received: from mail.uh.edu (SanJacinto.Mail.UH.EDU [129.7.69.101]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5QKjv5u005632 for ; Thu, 26 Jun 2003 16:45:57 -0400 Received: from conversion-daemon by mail.uh.edu (Sun Internet Mail Server sims.4.0.2001.07.26.11.50.p9) id <0HH300D01WCEN2-.at.-mail.uh.edu> for chemistry-.at.-ccl.net; Thu, 26 Jun 2003 15:45:50 -0500 (CDT) Received: from localhost (Colorado.Mail.UH.EDU [129.7.69.103]) by mail.uh.edu (Sun Internet Mail Server sims.4.0.2001.07.26.11.50.p9) with ESMTP id <0HH300D3XWCDI5-.at.-mail.uh.edu> for chemistry-.at.-ccl.net; Thu, 26 Jun 2003 15:45:49 -0500 (CDT) Date: Thu, 26 Jun 2003 15:45:49 -0500 (CDT) From: Niharendu.Choudhury-.at.-mail.uh.edu Subject: periodic boundary condition in CHARMM To: chemistry-.at.-ccl.net Message-id: <482369130.1056660349445.JavaMail.root@localhost> MIME-version: 1.0 X-Mailer: Sun(TM) Web Access 1.2 Content-type: text/plain; charset=ISO-8859-1 Content-transfer-encoding: 7BIT Hi ccl-users I am a new CHARMM user. In CHARMM (version c26b1) for liquid water simulation with PERIODIC BOUNDARY CONDITION in a cubic box with box length say 31.063 angstorm, if i use the following command is that okay. command i used: Crystal Define Cubic 31.063 31.063 90.0 90.0 90.0 Crystal Build noperations 0 Do the above commads mean coordinates of all the particles, those are out of the primary box, in EVERY dynamic TIME STEP will be set back in the primary simulation box? If so, then in my final output coordinate file, I found some coordinates which are outside the box, say -20.5 and 20.05 etc. Please explain. Nihar From chemistry-request@ccl.net Tue Jun 24 17:47:50 2003 Received: from amnapsmtp01.bp.com (amnapsmtp01.bp.com [208.251.247.82]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5OLlo5u006105 for ; Tue, 24 Jun 2003 17:47:50 -0400 Received: from amhouav002.bp.com (inetgate11.bp.com [63.118.26.162]) by amnapsmtp01.bp.com (Switch-3.0.4/Switch-3.0.0) with SMTP id h5OLtCO6025943 for ; Tue, 24 Jun 2003 16:55:16 -0500 (CDT) Received: from 149.178.200.224 by amhouav002.bp.com (InterScan E-Mail VirusWall NT); Tue, 24 Jun 2003 16:43:21 -0500 Received: by amnapx4.bp.com with Internet Mail Service (5.5.2653.19) id ; Tue, 24 Jun 2003 16:43:20 -0500 Message-ID: <21767B44B03F89458DB32821B57451AD026C1853_at_bp1napex002.bp1.ad.bp.com> From: "Golab, Joseph T" To: "'CHEMISTRY_at_ccl.net'" Cc: "'vesentini_at_biomed.polimi.it'" Subject: FW: Request about molecular modelling Date: Tue, 24 Jun 2003 16:47:44 -0500 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" CCL MEMBER: To the CCL List on behalf of these two Italian PHD students. It would be best to respond directly to Vesentini Simone "vesentini_at_biomed.polimi.it" but I will forward all the responses I receive. >> They are seeking hints on references to papers which discuss FF parameters for SO3- groups, preferably in proteins << Thanks in advance for any and all help you can relay to them. Joe ________________________________________________________________ Joseph T. Golab Phone: +1 (630) 961-7878 BP Naperville Complex, C-7 Fax: +1 (630) 420-4382 150 W. Warrenville Rd e-mail: GolabJT_at_BP.com Naperville, IL 60563 SOCON: 231 -----Original Message----- From: Vesentini Simone [mailto:vesentini_at_biomed.polimi.it] Sent: Wednesday, June 11, 2003 9:09 AM To: Golab, Joseph T Subject: Request about molecular modelling Dear Mr. Golab, we are two italian Ph.D. students from the Bioengineering Department of the Politecnico di Milano. One of our research areas is the developement of a multiscale model of tendons. For this purpose we are now focusing on the molecular modelling of some structural proteins (collagen) and polisaccharides (glycosamminoglycan) by means of the Cerius2 software. In particular, our goal is then evaluation of the force-elongation characteristic of glycosamminoglycans; we progressively stretch the molecule and evaluate its potential energy through a CVFF forcefields, which models the interaction between bonded atoms by means of a Morse potential. We are writing you the present e-mail because of a problem we still haven't overcome: we have no reliable information about the parameters we have to assign to the atoms of the SO3- groups which are part of glycosamminoglycans. Could you suggest us a reference we could refer to? We thank you in advance for your time and we send you our best regards. Yours Sincerely, Simone Vesentini Emiliano Votta From chemistry-request@ccl.net Tue Jun 24 13:17:05 2003 Received: from mailserver.unimi.it (mailserver.unimi.it [159.149.10.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5OHH45u000656 for ; Tue, 24 Jun 2003 13:17:05 -0400 Received: from smtp.unimi.it (smtp.unimi.it [159.149.10.3]) by mailserver.unimi.it (iPlanet Messaging Server 5.2 Patch 1 (built Aug 19 2002)) with ESMTP id <0HGZ00AK9XCI33^at^mailserver.unimi.it> for chemistry^at^ccl.net; Tue, 24 Jun 2003 19:17:06 +0200 (MEST) Received: from heisenberg.chimica.unimi.it (heisenberg.chimica.unimi.it [159.149.240.30]) by smtp.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with ESMTP id <0HGZ00LSSXCF9C^at^smtp.unimi.it> for chemistry^at^ccl.net; Tue, 24 Jun 2003 19:17:03 +0200 (MEST) Date: Tue, 24 Jun 2003 19:22:39 +0200 From: Alessandro Contini Subject: Re: CCL:local search in AutoDock In-reply-to: <3EF8BB49@webmail1> To: Robert Flight Cc: CCL Message-id: <200306241922.39557.alessandro.contini^at^unimi.it> Organization: Istituto di Chimica Organica "Alessandro Marchesini" MIME-version: 1.0 Content-type: text/plain; charset=iso-8859-1 Content-disposition: inline User-Agent: KMail/1.5.1 References: <3EF8BB49@webmail1> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h5OHH55u000661 Hi Robert, wat you are experiencing is probaly a bug in ADT. I don't know wich version you are using, but try to download the last one. I had the same problem a few month ago and I solved it by choosing a random start, because it seemed that ADT didn't recognize properly the ligand starting coordinates relative to the receptor file; the docking run was correct but there was some sort of offset between the ligand conformations and the receptor. By choosing a random start, If everything works fine, you should be able to properly reproduce your docking and to correctly visualize results. Hope this help Alessandro Contini Alle 15:07, martedl 24 giugno 2003, Robert Flight ha scritto: > Hi, > > I'm trying to use a local search (pseudo-sw) to minimize a docked pose of a > ligand into a receptor. When I look at the ligand and the receptor in ADT, > the ligand is in the correct starting position. The Grid box is large > enough to contain the search space. I'm using a non-random start, > non-random relative dihedral offset, and initial relative dihedrals, which > should all start the local search from the specified initial coordinates. > > The output ligand poses end up completely outside the docking box, and > outside the receptor as well, with an RMSD of 85 Angstroms!!! Can anyone > tell me what is happening, as I see no reason why the ligand should end up > outside the docking box! > > Thank you for your help, > > -Robert > > ******************************** > Robert Flight > Masters Student > Department of Chemistry > University of New Brunswick > Fredericton, NB Canada E3B 6E2 > e-mail: robert.flight^at^unb.ca > > ******************************** > > "People think it must be fun to be a super genius, but they don't realize > how hard it is to put up with all the idiots in the world." -Calvin from > Calvin & Hobbes > > > -= This is automatically added to each message by mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: > line and send your message to: CHEMISTRY^at^ccl.net > > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST^at^ccl.net HOME Page: http://www.ccl.net | Jobs Page: > http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jkl^at^ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ -- Alessandro Contini, Ph.D. Istituto di Chimica Organica "Alessandro Marchesini" Facolt` di Farmacia Universit` degli Studi di Milano Via Venezian, 21 20133 Milano Tel. +390250314480 Fax +390250314476 http://users.unimi.it/istchimorg/pagconthtm.htm ------------------------------------------------------------------- ------------------------------------------------------------------- This e-mail and any attachments is confidential and may contain attorney privileged information intended for the addressee(s) only. Reading, copying, disclosure or use by anybody else is unauthorised. If you are not the intended recipient, please delete this message and any attachments and advise the sender by return e-mail. ------------------------------------------------------------------- Il contenuto di questo messaggio elettronico e' riservato e tutelato dal segreto professionale ed e' rivolto eslusivamente al/ai destinatario/i identificato/i. Pertanto e' proibito leggerlo, copiarlo, divulgarlo o utilizzarlo da parte di chiunque salvo il/i destinatario/i. Se non siete il destinatario, vi invitiamo a cancellare il messaggio ed eventuali allegati dandocene immediatamente comunicazione scritta a mezzo posta elettronica. From chemistry-request@ccl.net Fri Jun 27 08:26:30 2003 Received: from lx00.istm.cnr.it (lx00.istm.cnr.it [155.253.3.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5RCQT5u021205 for ; Fri, 27 Jun 2003 08:26:30 -0400 Received: from localhost.localdomain (IDENT:uucp-.at.-localhost.localdomain [127.0.0.1]) by lx00.istm.cnr.it (8.11.6/8.11.6) with ESMTP id h5RCQRf20458 for ; Fri, 27 Jun 2003 14:26:27 +0200 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed Date: Fri, 27 Jun 2003 14:25:38 +0200 Disposition-Notification-To: Alessandro Ponti From: Alessandro Ponti Message-ID: <3EFC37C2.1070806-.at.-istm.cnr.it> MIME-Version: 1.0 Organization: CNR - CSRSRC Received: from istm.cnr.it (pc90.istm.cnr.it [155.253.3.190]) by lx00.istm.cnr.it (AvMailGate-2.0.0.6) id 20447-7AE50325; Fri, 27 Jun 2003 14:26:09 +0200 Subject: 16GB file problem in Gaussian To: chemistry-.at.-ccl.net User-Agent: Mozilla/5.0 (Windows; U; Win 9x 4.90; en-US; rv:1.4) Gecko/20030529 X-Accept-Language: en-us, en X-AntiVirus: OK! AntiVir MailGate Version 2.0.0.6 at lx00.istm.cnr.it has not found any known virus in this email. Dear All, recently I met with the problem that the maximum total RWF file length in Gaussian98 is 16GB. (NB: I'm not referring to the maxiumum file length allowed by your OS; such problem is solved by splitting the RWF into several small files). I met the 16GB problem while trying MP2 frequency, MP4 energy, and QCISD energy calculations. Apparently, Gaussian98 cannot deal with more than 16GB disk space, eg when you set MaxDisk=17GB. Looking at the route section, IOp(8/27) ("maximum amount of dik to use" in the four-index transformation) is negative and equal to -1GB (recall that IOp(8/27) is expressed in Words). Here's a small table of my experiments MaxDisk : 1 2 ... 15 16 17 ... 31 32 33 ... IOp(8/27) : 1 2 ... 15 -16 -15 ... -1 0 1 ... Perusing G98 manuals and source files was useless. After searching in the net, it seems that the 16GB problem is related to Gaussian98 addressing by 32-bit integers. At http://www.ccl.net/ASC/PET/CCM/skeleton/software/gaussian/gaussian-tips.html I found a brief text claiming this problem can be circumvented, at least partially: "The second limit has a less satisfactory workaround. Scratch data stored in the read-write file can be diverted into a separate file with the option %usescr while this does not evenly balance the usage it does allow specification of 32 GB of storage and depending on the type of calculation more or less complete utilization of this whole amount." However I did not really understand what it means. Does anyone knows how to overcome the 16GB limit? Has anyone information about this problem? Any little piece of information might be a precious clue to us. I thank you all in advance for any help. Bye Alessandro -- ******** NEW TELEPHONE NUMBER AND EMAIL ADDRESS ******** +------------------------------------------------------+ | Dr. Alessandro Ponti | | | | Consiglio Nazionale delle Ricerche | | Istituto di Scienze e Tecnologie Molecolari | | | | via Camillo Golgi 19 | Tel +39 02 5031 4280 | | I-20133 Milano | Fax +39 02 5031 4300 | | ITALY | email a.ponti.-at-.istm.cnr.it | | | www www.istm.cnr.it/~ponti | +------------------------------------------------------+ From chemistry-request@ccl.net Tue Jun 24 04:17:41 2003 Received: from shiva.jussieu.fr (shiva.jussieu.fr [134.157.0.129]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5O8HY5u017923 for ; Tue, 24 Jun 2003 04:17:41 -0400 Received: from ds10.itodys.jussieu.fr (ds10.itodys.jussieu.fr [134.157.24.13]) by shiva.jussieu.fr (8.12.9/jtpda-5.4) with ESMTP id h5O8HLv4096691 for ; Tue, 24 Jun 2003 10:17:27 +0200 (CEST) Received: by ds10.itodys.jussieu.fr (8.12.1/1.1.2.11/09Jul02-1200PM) id h5O8HKew265321; Tue, 24 Jun 2003 10:17:20 +0200 (MEST) Date: Tue, 24 Jun 2003 10:17:20 +0200 (MEST) From: Michel Petitjean Message-Id: <200306240817.h5O8HKew265321~at~ds10.itodys.jussieu.fr> To: chemistry~at~ccl.net Subject: CCL:Re: superimposing two moleculesvi mail.obj.1 X-Antivirus: scanned by sophie at shiva.jussieu.fr To: chemistry~at~ccl.net Subject: CCL:Re: superimposing two molecules!! The algorithm of Kabsch looks for an optimal orthogonal matrix rather than for a rotation. Thus mirror images are optimally superposed as if they were identical. Many solutions of the RMS superposition problem have been published since 1962 (see references cited in Comput. Chem. 1998,22[6],pp.463-5). You can download the ARMS and CSR freewares from the following site: http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#ARMS http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#CSR ARMS and CSR compute the optimal rotation (and translation). The documentations and references are also available from the site. ARMS reads data, assuming an implicit pairwise atomic correspondence (e.g. as it is usually done for protein backbones), then performs the superposition as in most commercial softwares, then computes the 3D common motif via the SDM algorithm (but you will not find SDM in any commercial software, although it is very simple to programme!). CSR do all what do ARMS, but has an automated pairwise atomic correspondance detection. Thus it works for any pair of general molecules, but runs slower than ARMS. Of course, no commercial software offers presently such kind of fully automated 3D common motif calculation. CSR is used by the Pasteur Institute (see their website). Michel Petitjean, Email: petitjean~at~itodys.jussieu.fr ITODYS (CNRS, UMR 7086) ptitjean~at~ccr.jussieu.fr 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 http://petitjeanmichel.free.fr/itoweb.petitjean.html Pradipta Bandyopadhyay wrote: >Hi, > > Does anyone have a code (in fortran), which superimposes two molecules? > I am looking for the implementation of the algorithm mentioned in the W. >Kabsch paper (Acta. Crys.A 32, 922). > >thanks. > > Pradipta From chemistry-request@ccl.net Tue Jun 24 19:42:12 2003 Received: from smtp2.server.rpi.edu (smtp2.server.rpi.edu [128.113.2.2]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5ONgC5u007480 for ; Tue, 24 Jun 2003 19:42:12 -0400 Received: from rpi.edu (omniocular-22.dynamic.rpi.edu [128.113.135.31]) by smtp2.server.rpi.edu (8.12.9/8.12.9) with ESMTP id h5ONg613001555; Tue, 24 Jun 2003 19:42:08 -0400 Message-ID: <3EF8E1E7.EFC7AC27!at!rpi.edu> Date: Tue, 24 Jun 2003 19:42:31 -0400 From: "Curt M. Breneman" X-Mailer: Mozilla 4.77 [en] (Win98; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry!at!ccl.net, qsar_society!at!accelrys.com Subject: Public Annoucement: ACS COMP Division "Emerging Technologies" Competitor List (Sponsored by Schrodinger) Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-CanItPRO-Stream: unclaimed-spam X-Scanned-By: CanIt (www . canit . ca) Dear Folks, The ACS Division of Computers in Chemistry is proud to announce the list of seven competitors for the Fall 2003 "Emerging Technologies in Computational Chemstry" (Co-sponsored by Schrodinger, Inc) to be held at the New York ACS Meeting. We thank everyone who entered the competition, and make note of the difficulty with which the following presentations were selected from a large pool of highly-qualified entries. The talks selected by a panel of experts are listed below (in no particular rank order): COMP 98 [669375]: Mining molecular dynamics data for molecular properties Ralph A. Wheeler, Department of Chemistry & Biochemistry, University of Oklahoma, 620 Parrington Oval, Norman, OK 73019 COMP 99 [661122]: A Super-linear Minimization Scheme for the Nudged Elastic Band Method Jhih-Wei Chu1, Bernhardt Trout1, and Bernard R. Brooks2. (1) Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, (2) Laboratory of Biophysical Chemistry, National Heart, Lung and Blood Institute, National Institutes of Health COMP 100 [645648]: Peptide to non-peptide: A real breakthrough in virtual screening Jeremy G. Vinter, Timothy J. Cheeseright, and Mark D. Mackey, Cresset BioMolecular Discovery, Spirella Building, Bridge Rd, SG 6 4ET, Letchworth, United Kingdom COMP 101 [664769]: Implementation and Development of the Self-Consistent Charge Density Functional Tight-Binding Method Maciej Gutowski, Fundamental Science Division, Pacific Northwest National Laboratory, 902 Battelle Blvd., P.O. Box 999, MS K1-96, Richland, WA 99352, COMP 102 [664273]: Prediction and classification of protein binding sites Matthias Keil1, Thomas Exner2, and J|rgen Brickman2. (1) Discovery Informatics, Tripos, Inc, 1699 South Hanley Road, St. Louis, MO 63144, (2) Department of Physical Chemistry, Darmstadt University of Technology COMP 103 [659400]: QSAR-based database mining: A success story of the discovery and experimental validation of novel anticonvulsant compounds Min Shen1, Cecile Beguin2, Alexander Golbraikh1, Harold Kohn2, and Alexander Tropsha1. (1) Laboratory for Molecular Modeling, School of Pharmacy, University of North Carolina, CB # 7360, Beard Hall, School of Pharmacy, Chapel Hill, NC 27599-7360, (2) Department of Medicinal Chemistry and Natural Products, School of Pharmacy, University of North Carolina at Chapel Hill COMP 104 [643901]: Stochastic proximity embedding methods and applications Huafeng Xu, and Dimitris K. Agrafiotis, Research Informatics, 3-Dimensional Pharmaceuticals, Inc, 8 Clarke Drive, Cranbury, NJ 08512 We hope to see you there in New York City in September! Curt Breneman RPI Chemistry COMP Treasurer Organizer, Emerging Technologies Symposium From chemistry-request@ccl.net Tue Jun 24 13:39:54 2003 Received: from udmercy.edu (udmercy.edu [198.109.24.100]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5OHdr5u001469 for ; Tue, 24 Jun 2003 13:39:54 -0400 Received: from [198.109.25.164] (account ) by udmercy.edu (CommuniGate Pro WebUser 3.1) with HTTP id 23962672; Tue, 24 Jun 2003 13:39:52 -0400 From: "Jonathan Stevens" Subject: Linux: splitting g98 rwf files To: chemistry~at~ccl.net X-Mailer: CommuniGate Pro Web Mailer v.3.1 Date: Tue, 24 Jun 2003 13:39:52 -0400 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="ISO-8859-1" I have run into a problem running CCSD(T) calculations with g98 on Linux systems. Specifically, the following eror message appears whenever a .rwf file is near 2 GB in size: Erroneous write during file extend. write 61439 instead of 4096 Probably out of disk space. Write error in NtrExt1 The computation is not really out of disk space (nearly 80 GB are free) I have been told that this is a problem with the Linux OS and may be circumvented by splitting the large g98 rwf file for the CCSD(T) calculation. Can anyone tell me how to do this? Thanks for any help you can give. Jonathan E. Stevens Department of Chemistry and Biochemistry University of Detroit Mercy 4001 W. McNichols Road P.O. Box 19900 Detroit, MI 48219-0900 313-993-1048 fax:313-993-1144 stevenje~at~udmercy.edu From chemistry-request@ccl.net Thu Jun 26 17:35:53 2003 Received: from kafka.net.nih.gov (kafka.net.nih.gov [165.112.130.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5QLZr5u006516 for ; Thu, 26 Jun 2003 17:35:53 -0400 Received: from pollux.cber.nih.gov (pollux.cber.nih.gov [128.231.52.5]) by kafka.net.nih.gov (8.12.9/8.12.9) with ESMTP id h5QLZrx9010474; Thu, 26 Jun 2003 17:35:53 -0400 (EDT) Date: Thu, 26 Jun 2003 17:03:05 -0400 From: Rick Venable To: wei cc: chemistry(at)ccl.net Subject: Re: help about charmm In-Reply-To: <200306261658.31539.weiz(at)mail.rochester.edu> Message-ID: References: <200306261658.31539.weiz(at)mail.rochester.edu> ReplyTo: Rick_Venable(at)nih.gov MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Thu, 26 Jun 2003, wei wrote: > I have a general question about charmm parameter file. for many > dihedral angles there are multiple terms for their potential function. > do I have to comment all the redundant terms before I do the > simulation? Definitely not. In most cases, the multiple terms have different periodicity, and represent several cosine functions being added together to best fit results from QM calculations on model compounds for the torsion in question. There is also multiplicity at branching points; for example, the chi1 sidechain torsion for many amino acids would have energy terms for both the N-CA-CB-CG torsion, as well as the C-CA-CB-CG torsion. This has been accounted for in the parameter development. =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= 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 ------------------------------------- "Don't blame me, I voted for Kang." Homer =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= From chemistry-request@ccl.net Tue Jun 24 12:14:59 2003 Received: from shiva.jussieu.fr (shiva.jussieu.fr [134.157.0.129]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5OGEr5u030509 for ; Tue, 24 Jun 2003 12:14:59 -0400 Received: from ds10.itodys.jussieu.fr (ds10.itodys.jussieu.fr [134.157.24.13]) by shiva.jussieu.fr (8.12.9/jtpda-5.4) with ESMTP id h5OGEpv4003410 for ; Tue, 24 Jun 2003 18:14:51 +0200 (CEST) Received: by ds10.itodys.jussieu.fr (8.12.1/1.1.2.11/09Jul02-1200PM) id h5OGEprd277920; Tue, 24 Jun 2003 18:14:51 +0200 (MEST) Date: Tue, 24 Jun 2003 18:14:51 +0200 (MEST) From: Michel Petitjean Message-Id: <200306241614.h5OGEprd277920$at$ds10.itodys.jussieu.fr> To: chemistry$at$ccl.net Subject: CCL:Re: superimposing two moleculesmail X-Antivirus: scanned by sophie at shiva.jussieu.fr To: chemistry$at$ccl.net Subject: CCL:Re: superimposing two molecules!! The algorithm of Kabsch looks for an optimal orthogonal matrix rather than for a rotation. Thus mirror images are optimally superposed as if they were identical. Many solutions of the RMS superposition problem have been published since 1962 (see references cited in Comput. Chem. 1998,22[6],pp.463-5). You can download the ARMS and CSR freewares from the following site: http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#ARMS http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#CSR ARMS and CSR compute the optimal rotation (and translation). The documentations and references are also available from the site. ARMS reads data, assuming an implicit pairwise atomic correspondence (e.g. as it is usually done for protein backbones), then performs the superposition as in most commercial softwares, then computes the 3D common motif via the SDM algorithm (but you will not find SDM in any commercial software, although it is very simple to programme!). CSR do all what do ARMS, but has an automated pairwise atomic correspondance detection. Thus it works for any pair of general molecules, but runs slower than ARMS. Of course, no commercial software offers presently such kind of fully automated 3D common motif calculation. CSR is used by the Pasteur Institute (see their website). Michel Petitjean, Email: petitjean$at$itodys.jussieu.fr ITODYS (CNRS, UMR 7086) ptitjean$at$ccr.jussieu.fr 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 http://petitjeanmichel.free.fr/itoweb.petitjean.html Pradipta Bandyopadhyay wrote: >Hi, > > Does anyone have a code (in fortran), which superimposes two molecules? > I am looking for the implementation of the algorithm mentioned in the W. >Kabsch paper (Acta. Crys.A 32, 922). > >thanks. > > Pradipta From chemistry-request@ccl.net Tue Jun 24 12:15:34 2003 Received: from shiva.jussieu.fr (shiva.jussieu.fr [134.157.0.129]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5OGFT5u030542 for ; Tue, 24 Jun 2003 12:15:34 -0400 Received: from ds10.itodys.jussieu.fr (ds10.itodys.jussieu.fr [134.157.24.13]) by shiva.jussieu.fr (8.12.9/jtpda-5.4) with ESMTP id h5OGFRv4003905 for ; Tue, 24 Jun 2003 18:15:27 +0200 (CEST) Received: by ds10.itodys.jussieu.fr (8.12.1/1.1.2.11/09Jul02-1200PM) id h5OGFQ25277910; Tue, 24 Jun 2003 18:15:26 +0200 (MEST) Date: Tue, 24 Jun 2003 18:15:26 +0200 (MEST) From: Michel Petitjean Message-Id: <200306241615.h5OGFQ25277910~at~ds10.itodys.jussieu.fr> To: chemistry~at~ccl.net Subject: CCL:Re: superimposing two moleculles X-Antivirus: scanned by sophie at shiva.jussieu.fr To: chemistry~at~ccl.net Subject: CCL:Re: superimposing two molecules!! The algorithm of Kabsch looks for an optimal orthogonal matrix rather than for a rotation. Thus mirror images are optimally superposed as if they were identical. Many solutions of the RMS superposition problem have been published since 1962 (see references cited in Comput. Chem. 1998,22[6],pp.463-5). You can download the ARMS and CSR freewares from the following site: http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#ARMS http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#CSR ARMS and CSR compute the optimal rotation (and translation). The documentations and references are also available from the site. ARMS reads data, assuming an implicit pairwise atomic correspondence (e.g. as it is usually done for protein backbones), then performs the superposition as in most commercial softwares, then computes the 3D common motif via the SDM algorithm (but you will not find SDM in any commercial software, although it is very simple to programme!). CSR do all what do ARMS, but has an automated pairwise atomic correspondance detection. Thus it works for any pair of general molecules, but runs slower than ARMS. Of course, no commercial software offers presently such kind of fully automated 3D common motif calculation. CSR is used by the Pasteur Institute (see their website). Michel Petitjean, Email: petitjean~at~itodys.jussieu.fr ITODYS (CNRS, UMR 7086) ptitjean~at~ccr.jussieu.fr 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 http://petitjeanmichel.free.fr/itoweb.petitjean.html Pradipta Bandyopadhyay wrote: >Hi, > > Does anyone have a code (in fortran), which superimposes two molecules? > I am looking for the implementation of the algorithm mentioned in the W. >Kabsch paper (Acta. Crys.A 32, 922). > >thanks. > > Pradipta From chemistry-request@ccl.net Tue Jun 24 03:22:46 2003 Received: from smtp.dmbr.UGent.be (dmbr242.fvms.ugent.be [157.193.189.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5O7Mk5u016443 for ; Tue, 24 Jun 2003 03:22:46 -0400 Received: from lmb032.ugent.be (lmb032.ugent.be [157.193.78.89]) by smtp.dmbr.UGent.be (Postfix) with ESMTP id 8C89468206; Mon, 23 Jun 2003 17:34:50 +0200 (CEST) Subject: Simple potential energy calculations in VMD From: Dominique Vlieghe To: vmd-l{at}ks.uiuc.edu Cc: chemistry{at}ccl.net Content-Type: text/plain Organization: Message-Id: <1056382485.17625.6.camel{at}LMB032.rug.ac.be> Mime-Version: 1.0 X-Mailer: Ximian Evolution 1.2.4 Date: 23 Jun 2003 17:34:45 +0200 Content-Transfer-Encoding: 7bit Hi all, Is it possible to do simple energy calculations within VMD (without prior energy minimisations and/or dynamics). Furthermore, is it possible to calculate energies between (atom) selections? Regards, Dominique -- ------------------------------ Dominique Vlieghe, Ph.D., Bioinformatics Core, Dept. Molecular Biomedical Research & V.I.B., Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium Tel.: 32-9-2648749 Fax.: 32-9-2645348 email:dominique.vlieghe{at}dmb.rug.ac.be www:http://www.dmb.rug.ac.be/ ------------------------------ From chemistry-request@ccl.net Tue Jun 24 05:32:53 2003 Received: from shiva.jussieu.fr (shiva.jussieu.fr [134.157.0.129]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5O9Wk5u019207 for ; Tue, 24 Jun 2003 05:32:52 -0400 Received: from ds10.itodys.jussieu.fr (ds10.itodys.jussieu.fr [134.157.24.13]) by shiva.jussieu.fr (8.12.9/jtpda-5.4) with ESMTP id h5O9WMv4077805 for ; Tue, 24 Jun 2003 11:32:31 +0200 (CEST) Received: by ds10.itodys.jussieu.fr (8.12.1/1.1.2.11/09Jul02-1200PM) id h5O9WLoh267924; Tue, 24 Jun 2003 11:32:21 +0200 (MEST) Date: Tue, 24 Jun 2003 11:32:21 +0200 (MEST) From: Michel Petitjean Message-Id: <200306240932.h5O9WLoh267924-.at.-ds10.itodys.jussieu.fr> To: chemistry-.at.-ccl.net Subject: CCL:Re: g03 and RedHat 7.3 on Pentium X-Antivirus: scanned by sophie at shiva.jussieu.fr To: CCL Subject: CCL:Re: g03 and RedHat 7.3 on Pentium I have never installed g03, but may I suggest you to look if their is or not accordance between the name of the routines in the object files or libraries, and their names in the calling sequences. For that, use the compiler flag which produces the map of the called routines (retrieve this flag with the man f77 command), and use the nm command to look in the object files what are the exact names of the stored entries. If there is a difference, either modify the sources or add interfaces to transmit arguments, provided that you have indeed the required object files and libraries. If there is accordance between calling names and called names, specify full path names of every object and library in the copmil+link command. Michel Petitjean, Email: petitjean-.at.-itodys.jussieu.fr ITODYS (CNRS, UMR 7086) ptitjean-.at.-ccr.jussieu.fr 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 http://petitjeanmichel.free.fr/itoweb.petitjean.html http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html ........................................................................... Bryan Putnam wrote: Greetings, Has anyone had success building Gaussian 03 (g03-B.03) on a Pentium II or III, using RedHat Linux 7.3, and Portland Group compiler 4.0-2 ? I see in the installation notes that Gaussian, Inc. says it will "NOT work" with versions of RedHat earlier than 8.0, but I don't know if that's the issue or not. g03 seems to compile OK, but when the build gets to the point where the executables are linked, for example, pgf77 -mp -O2 -tp p7 -Mreentrant -Mrecursive -Mnosave -Minfo \ -Mneginfo -time -fast -Munroll \ -Mvect=assoc,recog,cachesize:524288,prefetch,sse \ -fastsse -Mscalarsse -g -o g03 ml0.o util.so -lm -lc I get many undefined references of the form, /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_msync@GLIBC_2.0' I've reproduced the entire horrible list of them below. I've tried various things, building statically, dynamically, adding additional libraries, using the Portland version of pgcc, trying various versions of gcc, etc., but nothing seems to work. Any help or suggestions appreciated! Thanks, Bryan -- Bryan F. Putnam http://www-rcd.cc.purdue.edu/~bfp/ Young Hall bfp-.at.-purdue.edu ITaP Research Computing Services http://www.itap.purdue.edu/rcs/ 151 South Grant Street Voice: 765.496.8225 West Lafayette, IN 47906-3560 Fax: 765.494.0566 /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_msync@GLIBC_2.0' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_pwrite@GLIBC_2.1.3' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_system@GLIBC_2.0' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_pause@GLIBC_2.0' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_lseek@GLIBC_2.0' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_connect@GLIBC_2.0' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_open64@GLIBC_2.1.3' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_close@GLIBC_2.0' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_lseek64@GLIBC_2.1.3' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_accept@GLIBC_2.0' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_recvmsg@GLIBC_2.0' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_sendto@GLIBC_2.0' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_pread@GLIBC_2.1.3' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_pwrite64@GLIBC_2.1.3' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__rpc_thread_destroy@GLIBC_2.2.3' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_tcdrain@GLIBC_2.0' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_send@GLIBC_2.0' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_write@GLIBC_2.0' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__on_exit@GLIBC_2.0' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_longjmp@GLIBC_2.1' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_read@GLIBC_2.0' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_sigaction@GLIBC_2.2' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_fsync@GLIBC_2.0' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_nanosleep@GLIBC_2.0' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_fcntl@GLIBC_2.0' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_pread64@GLIBC_2.1.3' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_sendmsg@GLIBC_2.0' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_recvfrom@GLIBC_2.0' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_siglongjmp@GLIBC_2.1' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_open@GLIBC_2.0' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_recv@GLIBC_2.0' From chemistry-request@ccl.net Thu Jun 26 17:00:05 2003 Received: from antivirus1.its.rochester.edu (antivirus1.its.rochester.edu [128.151.57.50]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5QL055u005921 for ; Thu, 26 Jun 2003 17:00:05 -0400 Received: from antivirus1.its.rochester.edu (localhost [127.0.0.1]) by antivirus1.its.rochester.edu (8.12.9/8.12.4) with ESMTP id h5QKxumM014322 for ; Thu, 26 Jun 2003 16:59:56 -0400 (EDT) Received: from mail.rochester.edu (mail1.ats.rochester.edu [128.151.224.31]) by antivirus1.its.rochester.edu (8.12.9/8.12.4) with SMTP id h5QKxpeX014305; Thu, 26 Jun 2003 16:59:51 -0400 (EDT) Received: from frenkel.chem.rochester.edu (frenkel.chem.rochester.edu [128.151.195.84]) by mail.rochester.edu (8.12.9/8.12.1) with ESMTP id h5QKxnxd004359; Thu, 26 Jun 2003 16:59:49 -0400 (EDT) Content-Type: text/plain; charset="us-ascii" From: wei Reply-To: weiz!at!mail.rochester.edu Organization: university of rochester To: chemistry!at!ccl.net Subject: help about charmm Date: Thu, 26 Jun 2003 16:58:31 -0400 User-Agent: KMail/1.4.1 Cc: Rick Venable , Rick Venable MIME-Version: 1.0 Message-Id: <200306261658.31539.weiz!at!mail.rochester.edu> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h5QL055u005922 Hi, All: I have a general question about charmm parameter file. for many dihedral angles there are multiple terms for their potential function. do I have to comment all the redundant terms before I do the simulation? thanks Wei From chemistry-request@ccl.net Tue Jun 24 12:16:48 2003 Received: from shiva.jussieu.fr (shiva.jussieu.fr [134.157.0.129]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5OGGh5u030600 for ; Tue, 24 Jun 2003 12:16:48 -0400 Received: from ds10.itodys.jussieu.fr (ds10.itodys.jussieu.fr [134.157.24.13]) by shiva.jussieu.fr (8.12.9/jtpda-5.4) with ESMTP id h5OGGev4005071 ; Tue, 24 Jun 2003 18:16:40 +0200 (CEST) Received: by ds10.itodys.jussieu.fr (8.12.1/1.1.2.11/09Jul02-1200PM) id h5OGGcHk278036; Tue, 24 Jun 2003 18:16:38 +0200 (MEST) Date: Tue, 24 Jun 2003 18:16:38 +0200 (MEST) From: Michel Petitjean Message-Id: <200306241616.h5OGGcHk278036*at*ds10.itodys.jussieu.fr> To: <>, chemistry*at*ccl.net, mail.obj.1*at*jussieu.fr, moleculles*at*jussieu.fr, ptitjean*at*ccr.jussieu.fr, superimposing*at*jussieu.fr, two*at*jussieu.fr Subject: CCL:Re: superimposing two moleculesmail -s CCL:Re: X-Antivirus: scanned by sophie at shiva.jussieu.fr To: chemistry*at*ccl.net Subject: CCL:Re: superimposing two molecules!! The algorithm of Kabsch looks for an optimal orthogonal matrix rather than for a rotation. Thus mirror images are optimally superposed as if they were identical. Many solutions of the RMS superposition problem have been published since 1962 (see references cited in Comput. Chem. 1998,22[6],pp.463-5). You can download the ARMS and CSR freewares from the following site: http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#ARMS http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#CSR ARMS and CSR compute the optimal rotation (and translation). The documentations and references are also available from the site. ARMS reads data, assuming an implicit pairwise atomic correspondence (e.g. as it is usually done for protein backbones), then performs the superposition as in most commercial softwares, then computes the 3D common motif via the SDM algorithm (but you will not find SDM in any commercial software, although it is very simple to programme!). CSR do all what do ARMS, but has an automated pairwise atomic correspondance detection. Thus it works for any pair of general molecules, but runs slower than ARMS. Of course, no commercial software offers presently such kind of fully automated 3D common motif calculation. CSR is used by the Pasteur Institute (see their website). Michel Petitjean, Email: petitjean*at*itodys.jussieu.fr ITODYS (CNRS, UMR 7086) ptitjean*at*ccr.jussieu.fr 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 http://petitjeanmichel.free.fr/itoweb.petitjean.html Pradipta Bandyopadhyay wrote: >Hi, > > Does anyone have a code (in fortran), which superimposes two molecules? > I am looking for the implementation of the algorithm mentioned in the W. >Kabsch paper (Acta. Crys.A 32, 922). > >thanks. > > Pradipta From chemistry-request@ccl.net Tue Jun 24 14:22:38 2003 Received: from smtp4.dti.ne.jp (smtp4.dti.ne.jp [202.216.228.39]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5OIMa5u002769 for ; Tue, 24 Jun 2003 14:22:37 -0400 Received: from oemcomputer (PPP70.fukuoka-ip.dti.ne.jp [211.132.92.70]) by smtp4.dti.ne.jp (3.08s) with SMTP id h5OIMNAi020341 for ; Wed, 25 Jun 2003 03:22:25 +0900 (JST) Message-ID: <002401c33a7c$f4d28960$465c84d3@oemcomputer> From: "Telkuni" To: Subject: How to get the orbital symmetry using Gaussian TDDFT ? Date: Wed, 25 Jun 2003 03:18:00 +0900 MIME-Version: 1.0 Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Hello CCLres, I'm trying TDDFT calculation on two molecules which are Nitrotoluene (C8H10N) and Benzen with G98W A7 on Win98SE. ** Sorry this mail is long. Because I have added the inputs below. However my calculations( Opt -> TDDFT ) are finished normally, I can't get each MO's symmetry in the part of "Molecular Orbital Coefficients" of the output. ** I've sent same question to Gaussian.Inc, but there is no reply. The result what I want is including the symmetry A1G, E1U, ... like: 1 2 3 4 5 (A1G)--O (E1U)--O (E1U)--O (E2G)--O (E2G)--O EIGENVALUES -- -11.23480 -11.23423 -11.23423 -11.23299 -11.23299 But I always get the outputs without the MO symmetries: 1 2 3 4 5 O O O O O EIGENVALUES -- -14.33676 -10.21977 -10.18454 -10.17838 -10.17481 or 1 2 3 4 5 O O O O O EIGENVALUES -- -10.18905 -10.18878 -10.18878 -10.18823 -10.18823 (Modified "G98W exercise 9_04a input" is used as .) I can't find the reasons why I can't get the symmetry. Please help me. ...Any responses I'll appreciate and summarize them. Thanks in Advance. ******** Inputs ********* ///// Ex.A ////// %Chk=exa #T SVWN5/6-31G Opt Step1 Opting 0,1 C -0.072908 1.523961 0.000000 H 0.377522 2.530931 0.000000 C 0.746152 0.392531 0.000000 C 0.175802 -0.882499 0.000000 C -1.213578 -1.026079 0.000000 C -2.032628 0.105351 0.000000 C -1.462278 1.380381 0.000000 C 2.274212 0.550468 0.000000 N 1.035081 -2.069527 0.000000 H -1.663998 -2.033049 0.000000 H -3.129888 -0.008059 0.000000 H -2.109118 2.273951 0.000000 H 2.583600 1.099395 0.890639 H 2.742198 -0.435063 0.000002 H 2.583600 1.099393 -0.890641 H 2.044505 -1.965206 0.000000 H 0.620714 -2.995875 0.000000 --Link1-- %Chk=exa # TD(50-50) B3LYP/6-31G(d) Density Pop=Full SCF=NoVarAcc Guess=Read Geom=Check Step2 TDDFT 0,1 ///// Ex.B ///// %Chk=exb #T SVWN5/6-31G Opt Step1 Opting 0,1 C C,1,CC C,1,CC,2,120. C,2,CC,1,120.,3,0. C,3,CC,1,120.,2,0. C,4,CC,2,120.,1,0. H,1,CH,2,120.,4,180. H,2,CH,1,120.,7,0. H,3,CH,1,120.,7,0. H,4,CH,2,120.,8,0. H,5,CH,3,120.,9,0. H,6,CH,4,120.,10,0. CC=1.38616 CH=1.07560 --Link1-- %Chk=exb # TD(50-50) B3LYP/6-31G(d) SCF=NoVarAcc # Density Pop=Full Guess=Read Geom=Check IOP(9/40=3) Step2 TDDFT 0,1 ---------------------------------------------------- Telkuni Tsuru telkuni-.at.-venus.dti.ne.jp From chemistry-request@ccl.net Fri Jun 27 20:45:19 2003 Received: from york.smtp.ru (york.smtp.ru [62.118.249.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5S0jI5u018233 for ; Fri, 27 Jun 2003 20:45:19 -0400 Received: from [193.233.4.2] (account octy=at=smtp.ru HELO xr28-4) by york.smtp.ru (CommuniGate Pro SMTP 3.5.9) with ESMTP id 11048311 for chemistry=at=ccl.net; Sat, 28 Jun 2003 04:45:18 +0400 Date: Sat, 28 Jun 2003 04:43:47 -0700 From: octy X-Mailer: The Bat! (v1.61) Reply-To: octy-smtp X-Priority: 3 (Normal) Message-ID: <68735800184.20030628044347=at=smtp.ru> To: chemistry=at=ccl.net Subject: Re: CCL:AIM critical points analysis MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello Segio! These variables mean: Vnuc - The nuclear potential distribution; V - The potential energy density - trace of the stress vector; L(r) - Just the Laplcian of RHO If you use AIMPACK you can find some interesting information on the official site: http://www.chemistry.mcmaster.ca/aimpac/summary/summary.htm > Dear colleagues, > > I am trying to analyse the critical points for a molecule, > but I didn't found the exact meaning of some variables as > L(r), Vnuc(r) and V(r). > > Thank you very much in advance, > > Sergio Galembeck -- Best regards, Ivan Fedyanin mailto:octy=at=smtp.ru From chemistry-request@ccl.net Fri Jun 27 20:48:10 2003 Received: from york.smtp.ru (york.smtp.ru [62.118.249.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5S0m95u018301 for ; Fri, 27 Jun 2003 20:48:10 -0400 Received: from [193.233.4.2] (account octy_at_smtp.ru HELO xr28-4) by york.smtp.ru (CommuniGate Pro SMTP 3.5.9) with ESMTP id 11048656 for chemistry_at_ccl.net; Sat, 28 Jun 2003 04:48:10 +0400 Date: Sat, 28 Jun 2003 04:46:39 -0700 From: octy X-Mailer: The Bat! (v1.61) Reply-To: octy-smtp X-Priority: 3 (Normal) Message-ID: <78735972091.20030628044639_at_smtp.ru> To: chemistry_at_ccl.net Subject: CCL: Re: AIM critical points analysis MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello Segio! These variables mean: Vnuc - The nuclear potential distribution; V - The potential energy density - trace of the stress vector; L(r) - Just the Laplcian of RHO If you use AIMPACK you can find some interesting information on the official site: http://www.chemistry.mcmaster.ca/aimpac/summary/summary.htm > Dear colleagues, > > I am trying to analyse the critical points for a molecule, > but I didn't found the exact meaning of some variables as > L(r), Vnuc(r) and V(r). > > Thank you very much in advance, > > Sergio Galembeck -- Best regards, Ivan Fedyanin mailto:octy_at_smtp.ru