From jerry@dft.chem.cuhk.hk Tue Feb 27 08:30:59 1996 Received: from iris.chem.cuhk.hk for jerry@dft.chem.cuhk.hk by www.ccl.net (8.7.1/950822.1) id HAA29728; Tue, 27 Feb 1996 07:38:39 -0500 (EST) Received: from dft.chem.cuhk.hk by iris.chem.cuhk.hk via SMTP (931110.SGI/940406.SGI.AUTO) for chemistry@www.ccl.net id AA03161; Tue, 27 Feb 96 20:38:06 +0800 Received: by dft (950511.SGI.8.6.12.PATCH526/930416.SGI.AUTO) id UAA16929; Tue, 27 Feb 1996 20:38:04 +0800 Date: Tue, 27 Feb 1996 20:38:04 +0800 (HKT) From: Jerry C C Chan To: chemistry@www.ccl.net Subject: DFT package for chemical shielding Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear everyone, I would like to know what commercial available softwares which can be used to calculate the chemical shielding constants of transition metal using Density Functional Theory method, in addition to Gaussian94 and deMon1p0? Thanks in advance for your help. Jerry C.C. Chan jerry@dft.chem.cuhk.hk From robert@europa.chem.uga.edu Tue Feb 27 10:30:59 1996 Received: from europa.chem.uga.edu for robert@europa.chem.uga.edu by www.ccl.net (8.7.1/950822.1) id JAA00965; Tue, 27 Feb 1996 09:39:43 -0500 (EST) Received: from europa (robert@localhost [127.0.0.1]) by europa.chem.uga.edu (8.6.12/8.6.9) with SMTP id JAA03126; Tue, 27 Feb 1996 09:37:59 -0500 Sender: robert@europa.chem.uga.edu Message-ID: <31331746.59DBDBE9@europa.chem.uga.edu> Date: Tue, 27 Feb 1996 09:37:58 -0500 From: Jenn-Huei Lii Organization: Computational Center for Molecular Structure and Design (CCMSD) X-Mailer: Mozilla 2.0 (X11; I; Linux 1.3.15 i586) MIME-Version: 1.0 To: SUBRAPS@texaco.com CC: chemistry@www.ccl.net Subject: Re: CCL:Re: CCL:Dipole-Dipole Interaction in Dynamics References: <9602231650.AA29565@hyper.hyper.com> Content-Type: text/plain; charset=big5 Content-Transfer-Encoding: 7bit > Date: 21 Feb 1996 07:18:07 GMT > From: SUBRAPS@texaco.com > > Is there a Molecular Dynamics Package which incorporates dipole-dipole > interaction in the electrostatic computation?. > I would appreciate any input in this regard. > Please try Allinger's MM3(94) packages. Robert From george@cray.com Tue Feb 27 11:31:05 1996 Received: from timbuk.cray.com for george@cray.com by www.ccl.net (8.7.1/950822.1) id LAA03321; Tue, 27 Feb 1996 11:03:03 -0500 (EST) Received: from ironwood.cray.com (root@ironwood-fddi.cray.com [128.162.21.36]) by timbuk.cray.com (8.6.12/CRI-gate-8-2.11) with ESMTP id KAA24687 for ; Tue, 27 Feb 1996 10:02:59 -0600 Received: from archimedes (george@archimedes [128.162.171.10]) by ironwood.cray.com (8.6.12/CRI-ccm_serv-8-2.8) with SMTP id KAA08199 for ; Tue, 27 Feb 1996 10:02:58 -0600 From: George Fitzgerald Received: by archimedes (5.0/btd-b3) id AA10961; Tue, 27 Feb 1996 10:02:56 +0600 Message-Id: <9602271602.AA10961@archimedes> Date: Tue, 27 Feb 1996 10:02:56 +0600 To: chemistry@www.ccl.net Subject: CCL:G:DFT package for chemical shielding X-Mailer: [XMailTool v3.1.2] Jerry, The UniChem package available from Cray can compute NMR chemical shifts and shielding tensors using DFT. The method is similar to that published by Salahub for his 'uncoupled' approximation and uses either IGLO or LORG. Results from this method are generally pretty good for C; experience with other elements is limited. Sincerely, George Fitzgerald ======================================================= George Fitzgerald Cray Research, Inc. george@cray.com UniChem Manager 655E Lone Oak Dr. 1-612-683-3676 Eagan, MN 55121 1-612-683-3099 (fax) ======================================================= From dkwm2@cus.cam.ac.uk Tue Feb 27 12:31:04 1996 Received: from bootes.cus.cam.ac.uk for dkwm2@cus.cam.ac.uk by www.ccl.net (8.7.1/950822.1) id LAA05785; Tue, 27 Feb 1996 11:35:12 -0500 (EST) Received: from apus.cus.cam.ac.uk [131.111.8.2] (ident = root) by bootes.cus.cam.ac.uk with smtp (Smail-3.1.29.0 #36) id m0trSMC-000C1rC; Tue, 27 Feb 96 16:34 GMT Received: by apus.cus.cam.ac.uk (Smail-3.1.29.0 #36) id m0trSMB-000343C; Tue, 27 Feb 96 16:34 GMT Sender: dkwm2@cus.cam.ac.uk (D.K.W. Mok) Date: Tue, 27 Feb 1996 16:34:31 +0000 (GMT) From: Daniel Mok X-Sender: dkwm2@apus.cus.cam.ac.uk To: CHEMISTRY@www.ccl.net Subject: TCGMSG for SGI Power Challenge? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, I've used US GAMESS before. It was parallelized using TCGMSG routines. The TCGMSG can be compiled after editing the Makefile. However, it has porblem when programs start up and try to create child process. Anyone has used TCGMSG in SGI Power Challenge beofer? Daniel ******************************************************************************** * Daniel K.W. Mok * * E-Mail: dkwm2@cam.ac.uk Phone: 01223-336423 * * Office: Dept. of Chemistry, University of Cambridge * * Lensfield Rd., Cambridge CB2 1EW, UK. * ******************************************************************************** From cheidel@weizen.mpibpc.gwdg.de Tue Feb 27 13:31:15 1996 Received: from weizen.mpibpc.gwdg.de for cheidel@weizen.mpibpc.gwdg.de by www.ccl.net (8.7.1/950822.1) id MAA10086; Tue, 27 Feb 1996 12:57:22 -0500 (EST) Message-Id: <199602271757.MAA10086@www.ccl.net> Received: by weizen.mpibpc.gwdg.de (1.37.109.16/16.2) id AA194213825; Tue, 27 Feb 1996 18:57:05 +0100 Date: Tue, 27 Feb 1996 18:57:05 +0100 From: Christoph Heidelbach To: chemistry@www.ccl.net Subject: MD parameters from ab initio Cc: cheidel@gwdg.de Hallo everybody out there, I am searching for some information about the evaluation of force field parameters for molecular dynamics from ab initio or semiempirical calculations. What I am looking for is how to fit atomic charges and Lennard-Jones-parameters. Any answers will be greatly appreciated and I will summerize all replies. Best regards. Christoph ___________________________________________________________________________ Dipl.-Chem. Christoph Heidelbach Max-Planck-Institut fuer biophysikalische Chemie Am Fassberg 11 D-37077 Goettingen Tel. : (+551) 201 1339 Fax : (+551) 201 1341 E-Mail.: cheidel@weizen.mpibpc.gwdg.de cheidel@gwdg.de ____________________________________________________________________________ From v_uk@iris23.biosym.com Tue Feb 27 15:31:03 1996 Received: from bioc1.biosym.com for v_uk@iris23.biosym.com by www.ccl.net (8.7.1/950822.1) id OAA15664; Tue, 27 Feb 1996 14:50:56 -0500 (EST) Received: from iris23.biosym.com by bioc1.biosym.com (5.64/0.0) id AA17199; Tue, 27 Feb 96 11:55:09 -0800 Received: by iris23.biosym.com (940816.SGI.8.6.9/930416.SGI) for CHEMISTRY@www.ccl.net id LAA27142; Tue, 27 Feb 1996 11:50:40 -0800 Date: Tue, 27 Feb 1996 11:50:40 -0800 From: v_uk@biosym.com (Masahiko Katagari XPIRE 4-15-96 HOST John Newsam Tohoku University) Message-Id: <199602271950.LAA27142@iris23.biosym.com> To: CHEMISTRY@www.ccl.net Subject: APW Dear Collegues, Does anybody out there know any free APW program? Any information will be appreciated. Thanks in advance. Masahiko Katagiri Masahiko Katagiri, PhD. v_uk@biosym.com TEL -1-619-546-5389(direct) FAX -1-619-458-0136 e_mail v_uk@biosym.com MSI 9685 Scranton Road San Diego, CA 92121 From omar@boston.sgi.com Tue Feb 27 15:42:45 1996 Received: from sgi.sgi.com for omar@boston.sgi.com by www.ccl.net (8.7.1/950822.1) id PAA15817; Tue, 27 Feb 1996 15:12:09 -0500 (EST) Received: from sgihub.corp.sgi.com by sgi.sgi.com via ESMTP (950405.SGI.8.6.12/910110.SGI) for <@external-mail-relay.sgi.com:CHEMISTRY@www.ccl.net> id LAA18631; Tue, 27 Feb 1996 11:59:41 -0800 Received: from deliverator.sgi.com by sgihub.corp.sgi.com via ESMTP (950511.SGI.8.6.12.PATCH526/911001.SGI) for id LAA27008; Tue, 27 Feb 1996 11:59:40 -0800 Received: from sgihub.corp.sgi.com by deliverator.sgi.com via ESMTP (951211.SGI.8.6.12.PATCH1042/951211.SGI.AUTO) id LAA28294; Tue, 27 Feb 1996 11:59:39 -0800 Received: from sgibos.boston.sgi.com by sgihub.corp.sgi.com via SMTP (950511.SGI.8.6.12.PATCH526/911001.SGI) id LAA26995; Tue, 27 Feb 1996 11:59:34 -0800 Received: from arkham.boston.sgi.com by sgibos.boston.sgi.com via SMTP (931110.SGI/940406.SGI) for @sgihub.corp.sgi.com:dkwm2@cam.ac.uk id AA19654; Tue, 27 Feb 96 14:59:25 -0500 Received: by arkham.boston.sgi.com (951211.SGI.8.6.12.PATCH1042/951211.SGI) id OAA19455; Tue, 27 Feb 1996 14:59:19 -0500 From: "Omar G. Stradella" Message-Id: <9602271459.ZM19453@arkham.boston.sgi.com> Date: Tue, 27 Feb 1996 14:59:18 -0500 In-Reply-To: Daniel Mok "CCL:TCGMSG for SGI Power Challenge?" (Feb 27, 4:34pm) References: Organization: Silicon Graphics, Inc. Reply-To: omar@boston.sgi.com X-Mailer: Z-Mail (3.2.2 10apr95 MediaMail) To: Daniel Mok , CHEMISTRY@www.ccl.net Subject: Re: CCL:TCGMSG for SGI Power Challenge? Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii On Feb 27, 4:34pm, Daniel Mok wrote: > Subject: CCL:TCGMSG for SGI Power Challenge? > Dear Netters, > > I've used US GAMESS before. It was parallelized using TCGMSG routines. > The TCGMSG can be compiled after editing the Makefile. However, it has > porblem when programs start up and try to create child process. Anyone > has used TCGMSG in SGI Power Challenge beofer? > > Daniel Daniel, You can get TCGMSG for the R8000 from our anonymous ftp site: ftp.sgi.com:/pub/tcgmsg.4.04.r8k.tar.Z Omar. -- +-------------------------------------------------------------------+ Omar G. Stradella, Ph.D. Silicon Graphics, Inc. E-mail: omar@boston.sgi.com Computational Chemistry Phone: +1-(508) 567-2258 http://www.sgi.com/ChemBio FAX: +1-(508) 562-4755 http://reality.sgi.com/employees/omar +------ Ph-nglui mglw'nafh Cthulhu R'lyeh wgah'nagl fhtagn -------+ From nash@chem.wisc.edu Tue Feb 27 16:31:04 1996 Received: from audumla.students.wisc.edu for nash@chem.wisc.edu by www.ccl.net (8.7.1/950822.1) id PAA16287; Tue, 27 Feb 1996 15:53:50 -0500 (EST) Received: from caseyir by audumla.students.wisc.edu; id OAA114641; 8.6.9W/42; Tue, 27 Feb 1996 14:53:48 -0600 Date: Tue, 27 Feb 1996 14:53:48 -0600 Message-Id: <199602272053.OAA114641@audumla.students.wisc.edu> X-Sender: jrnash@students.wisc.edu X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: CHEMISTRY@www.ccl.net From: "John R. Nash" Subject: G: QST2 input To all Gaussian Gurus: I'm trying to run a QST2 job using g94, and the program seems to be hanging in link 101 (reading the molecular specification). The log file stops after the last atom of molecule 2 is read in. No error message, and the computer tells me that I'm perpetually in L101. I followed the instructions in the manual of making my input look like: %mem=... %chk=... #HF/STO-3G OPT=QST2 Title1 0 1 [z-matrix 1] Variables: [variables 1] Title2 0 1 [z-matrix 2] Variables: [variables 2] Interestingly, using the old LST keyword with otherwise identical input works. Since the input format for both methods is the same, as described in the manual, this is curious. Am I missing something? -john nash -==-John R. Nash-==-nash@chem.wisc.edu-==-Dept of Chemistry, UW-Madison-==- From howardp@syrres.com Tue Feb 27 17:31:05 1996 Received: from syrres.syrres.com for howardp@syrres.com by www.ccl.net (8.7.1/950822.1) id RAA16783; Tue, 27 Feb 1996 17:02:10 -0500 (EST) Date: Tue, 27 Feb 96 16:58 EST Message-ID: <9602271658.AA29104@syrres.syrres.com> Received: from syrres.com by syrres.syrres.com; Tue, 27 Feb 96 16:58 EST X-Sender: howardp@syrres.com X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: Phil Howard Subject: CCL:logP > From: Jauoad El Bahraoui > > Please tell me about programs does permit the calculation of the > partition coefficients octanol-water (logP) ? Our LOGKOW program calculates log Kow using atom-fragments (J Pharm Sci 84:83-92 (1995) with a mean error of 0.31 log units. It uses smaller fragments than the CLOGP and therefore, does not have a missing fragment problem. An order form for a free demo disk is available on our homepage, http://esc.syrres.com. Philip H. Howard Phone: 315-426-3350 Environmental Sciences Center Fax: 315-426-3429 Syracuse Research Corporation Email: howardp@syrres.com Merrill Lane Syracuse, NY 13210 From vis@gensia.com Tue Feb 27 18:31:04 1996 Received: from gtc05f for vis@gensia.com by www.ccl.net (8.7.1/950822.1) id RAA17165; Tue, 27 Feb 1996 17:39:03 -0500 (EST) Received: from genny (genny.res.gensia.com) by gtc05f (5.x/SMI-SVR4) id AA27175; Tue, 27 Feb 1996 14:32:59 -0800 Received: by genny (940816.SGI.8.6.9/930416.SGI.AUTO) id WAA02829; Tue, 27 Feb 1996 22:30:21 GMT Date: Tue, 27 Feb 1996 14:30:21 +48000 From: Viswanadhan To: CHEMISTRY@www.ccl.net Subject: On the binding of a Rigid Ligand vs. Flexible Analog to a receptor Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters: I have a problem that is fairly typical in pharmaceutical drug design, but is not easy to answer. We have a fairly rigid cyclic molecule (C) which can exist in two conformations (puckers), C1 and C2. Its acyclic analog (A) can also exist in different conformations, but they are not separated by high barriers. C1 and some conformers of A appear to have good interactions with a protein, but not C2. In terms of binding geometry/energies C1 is better than A but A is much better than C2. C1 and C2 are separated by a high barrier, but they are isoenergetic (internal energy from QM calculations). TCP (free energy perturbation) calculations for the mutation C1 -> A (or C2 -> A) will not reveal much because of the high barrier between C1 and C2 (making interconversion almost impossible in a reasonable time). Do you think it is possible to qualitatively assess the binding of C vs. A ? Does it help to calculate the barrier C1 to C2, accurately? (via ab initio or MOPAC)? I will summarize your responses as well as my thoughts on the problem. vis vis@gensia.com From vis@gensia.com Tue Feb 27 18:34:29 1996 Received: from gtc05f for vis@gensia.com by www.ccl.net (8.7.1/950822.1) id SAA17419; Tue, 27 Feb 1996 18:18:51 -0500 (EST) Received: from genny (genny.res.gensia.com) by gtc05f (5.x/SMI-SVR4) id AA27360; Tue, 27 Feb 1996 15:12:52 -0800 Received: by genny (940816.SGI.8.6.9/930416.SGI.AUTO) id XAA02880; Tue, 27 Feb 1996 23:10:04 GMT Date: Tue, 27 Feb 1996 15:10:03 +48000 From: Viswanadhan To: CHEMISTRY@www.ccl.net Subject: Binding of Flexible vs. Rigid ligands to a receptor Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters: I have a problem that is fairly typical in pharmaceutical drug design, but is not easy to solve. We have a fairly rigid cyclic molecule (C) which can exist in two conformations (puckers), C1 and C2. Its acyclic analog (A) can also exist in different conformations, but they are not separated by high barriers. C1 and some conformers of A appear to have good interactions with a protein, but not C2. In terms of binding geometry/energies C1 is better than A but A is much better than C2. C1 and C2 are separated by a high barrier, but they are isoenergetic (internal energy from QM calculations). TCP (free energy perturbation) calculations for the mutation C1 -> A (or C2 -> A) will not reveal much because of the high barrier between C1 and C2 (making interconversion almost impossible in a reasonable time). Do you think it is possible to qualitatively assess the binding of C vs. A ? Does it help to calculate the barrier C1 to C2, accurately? (via ab initio or MOPAC)? I will summarize your responses as well as my thoughts on the problem. vis vis@gensia.com