From chemistry-request@server.ccl.net Thu Nov 25 08:09:42 1999 Received: from mailhost.rdg.ac.uk (exim@sumh1.rdg.ac.uk [134.225.16.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA05289 for ; Thu, 25 Nov 1999 08:09:42 -0500 Received: from indyp.chemistry ([134.225.168.35] helo=reading.ac.uk) by mailhost.rdg.ac.uk with esmtp (University of Reading Email Service) id {11qxdN-0000Iw-00} for CHEMISTRY@www.ccl.net; Thu, 25 Nov 1999 12:04:21 +0000 Sender: dave@ccl.net Message-ID: <383D25E6.FC365E56@reading.ac.uk> Date: Thu, 25 Nov 1999 12:04:54 +0000 From: Dave Price Organization: none-what-so-ever X-Mailer: Mozilla 4.7 [en] (X11; I; IRIX 6.5 IP22) X-Accept-Language: en MIME-Version: 1.0 To: Comp Chem Mailing List Subject: Problem running g94 on Irix 6.5 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear All, I have compiled g94 on an SGI Indy R5000 under Irix 6.5.1. However, when I try to run it on a similar machine (R5000 Irix 6.5.1) I get this error- Local:indyp 20 % g94 < com/test000.com > sgi/test000.log 5523:g94: rld: Fatal Error: Cannot Successfully Map soname 'libblas.so' under any of the filenames /usr/scratch/indigog/g94/g94s/bsd/libblas.so:/usr/scratch/indigog/g94/g94/bsd/libblas.so:/usr/scratch/indigog/g94/g94s/private/libblas.so:/usr/scratch/indigog/g94/g94/private/libblas.so:/usr/scratch/indigog/g94/g94s/libblas.so:/usr/scratch/indigog/g94/g94/libblas.so:/usr/lib32/libblas.so:/usr/lib32/internal/libblas.so:/lib32/libblas.so:/opt/lib32/libblas.so:/usr/scratch/indigog/g94/g94s/bsd/libblas.so.1:/usr/scratch/indigog/g94/g94/bsd/libblas.so.1:/usr/scratch/indigog/g94/g94s/private/libblas.so.1:/usr/scratch/indigog/g94/g94/private/libblas.so.1:/usr/scratch/indigog/g94/g94s/libblas.so.1:/usr/scratch/indigog/g94/g94/libblas.so.1:/usr/lib32/libblas.so.1:/usr/lib32/internal/libblas.so.1:/lib32/libblas.so.1:/opt/lib32/libblas.so.1: But- Local:indyp 21 % whereis libblas.so libblas: /usr/lib/libblas.so /usr/lib/libblas.a /usr/share/catman/p_man/cat3/libblas Help? Cheers, Dave -- ------------------------------------------------------------------------ Dr. David W. Price, Tel: +44 (0)118 9875123 extn 7415 Department of Chemistry, Fax: +44 (0)118 9316331 University of Reading, mailto:d.w.price@reading.ac.uk Whiteknights, READING http://www.chem.rdg.ac.uk/g50/mmrg/dave/dave.html RG6 6AD U.K. ------------------------------------------------------------------------ From chemistry-request@server.ccl.net Fri Nov 26 11:48:08 1999 Received: from dedalus.lcc.ufmg.br (dedalus.lcc.ufmg.br [150.164.65.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA12061 for ; Fri, 26 Nov 1999 11:47:56 -0500 Received: from localhost (noronha@localhost) by dedalus.lcc.ufmg.br (8.9.3/8.9.3) with SMTP id NAA49490 for ; Fri, 26 Nov 1999 13:42:02 -0200 Date: Fri, 26 Nov 1999 13:42:01 -0200 (BDB) From: antonio luiz oliveira de noronha To: chemistry@ccl.net Subject: BeoWolf Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII CCL friends Where may I find information about how to build a beowolf cluster, his capabilities and other information?? Best regards ___________________________________________________________________ | | |Antonio Luiz Oliveira de Noronha - noronha@dedalus.lcc.ufmg.br | |Medicinal Chemistry of Organotin Compounds | |NEQUIM - Medicinal Chemistry Group | |Chemistry Departament - DQ | |UFMG - Federal University of Minas Gerais - Brazil | |Av. Antonio Carlos, 6627 - Campus Pampulha | |CEP 31270-901 - Belo Horizonte - MG - Brazil | |VOICE +55 31 499 5765 - FAX +55 31 499 5700 | |___________________________________________________________________| From chemistry-request@server.ccl.net Fri Nov 26 12:06:01 1999 Received: from MFD42U02.U-3MRS.FR (MFD42U02.U-3MRS.FR [193.51.220.34]) by server.ccl.net (8.8.7/8.8.7) with SMTP id MAA12173 for ; Fri, 26 Nov 1999 12:06:00 -0500 Received: from carro.u-3mrs.fr (localhost [127.0.0.1]) by MFD42U02.U-3MRS.FR (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id RAA12126 for ; Fri, 26 Nov 1999 17:12:35 +0100 Sender: ccl@MFD42U02.U-3MRS.FR Message-ID: <383EB172.41C6@carro.u-3mrs.fr> Date: Fri, 26 Nov 1999 17:12:34 +0100 From: Computational chemistry list X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX 6.3 IP32) MIME-Version: 1.0 To: chemistry@ccl.net Subject: boron PM3 parameters Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear ccl'ers I would like to know if boron PM3 parameters exists, and boron-magnesium parameters. Thanks -- ***************************************************************** SREP Laboratory Structure et reactivite des especes paramagnetiques Groupe de chimie theorique Universite de Provence, Marseille, France E-mail: ccl@carro.u-3mrs.fr Phone # : (ext) + 04-91-28-84-14 FAX # : (ext) + 04-91-98-85-12 ***************************************************************** From chemistry-request@server.ccl.net Fri Nov 26 12:28:37 1999 Received: from mail-b.bcc.ac.uk (mail-b.bcc.ac.uk [144.82.100.22]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA12300 for ; Fri, 26 Nov 1999 12:28:37 -0500 Received: from biochem.ucl.ac.uk (actually host bsmori1.biochem.ucl.ac.uk) by mail-b.bcc.ac.uk with SMTP (XT-PP) with ESMTP; Fri, 26 Nov 1999 16:22:42 +0000 Received: from bsmir18.biochem.ucl.ac.uk (bsmir18 [128.40.46.21]) by biochem.ucl.ac.uk (8.9.2/8.9.1) with ESMTP id QAA15894 for ; Fri, 26 Nov 1999 16:22:53 GMT Received: from localhost (nobeli@localhost) by bsmir18.biochem.ucl.ac.uk (8.9.3/8.9.3) with SMTP id QAA07155 for ; Fri, 26 Nov 1999 16:22:53 GMT X-Authentication-Warning: bsmir18.biochem.ucl.ac.uk: nobeli owned process doing -bs Date: Fri, 26 Nov 1999 16:22:53 +0000 ("GMT) From: Irene Nobeli X-Sender: nobeli@bsmir18 To: Computational Chemistry List Subject: Answers to : Dock and lone pairs Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I summarise the answers I received to my question on how DOCK treats lone pairs. Many thanks to the people who helped me out. My question was: >>>>>>>>>> Could any Dock 4.0 user please help me with this? I am one of these unfortunate people who try to use DOCK 4.0 without having Sybyl available to prepare the receptor and ligand files. I tried to use InsightII instead but I ran into the following problem: I load the protein (receptor) in InsightII, add hydrogens, and attempt to assign charges using the AMBER force field. However, charges seem to be only properly assigned, if I also allow lone pairs to be added. Can DOCK deal with lone pair sites? Am I supposed to use this mol2 file (with H and lone pairs) in the grid calculation, and then use the original (with no H and no lone pairs) for docking? Also, if anyone knows a discussion list for DOCK users, could they please send me an address? >>>>>>>>>>>>>> and the answers: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> From yadavm@scripps.edu Wed Nov 24 15:12:56 1999 Date: Wed, 24 Nov 1999 07:12:43 -0800 (PST) From: Maneesh Yadav Hi Irene, The only thing that is used for dock is the energy grid and sphere appoximation of the active site, generate the grid after potentials are assigned from the forcefield. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> From antony@dina.kvl.dk Wed Nov 24 15:57:33 1999 Date: Wed, 24 Nov 1999 16:57:23 +0100 (MET) From: Jens Antony You are perfectly right to my mind. The receptor in DOCK is represented by two entities: - a set of spheres which represent the geometry of the proposed binding site and - a grid enclosing the spheres which is used for energy calculation. The .mol2 file only enters into the grid calculation. The spheres are generated directly from the pdb file. Therefore lone pairs should not constitute a difficulty for DOCK in principle as long as the potentials are set reasonably. However, you should be aware that the calculated binding in DOCK energy is very approximate. > Also, if anyone knows a discussion list for DOCK users, could they please > send me an address? dock@francisco.ucsf.edu is a very useful email address where you can direct your technical questions to. You are probably familiar with the official DOCK www page: http://www.cmpharm.ucsf.edu/kuntz/dock.html. Hope it helps, Jens >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> From todd.ewing@camitro.com Wed Nov 24 16:59:32 1999 From: Todd Ewing Lone pairs in the mol2 file for grid input should be no problem, just make sure that the LP atom type exists in your vdw.defn file and that it has a non-zero but small radius and well-depth. Also make a molecular surface for the protein with no hydrogens or lone pairs using ms with MIDAS package or QCPE, and use that for sphgen input. Good luck! Todd From chemistry-request@server.ccl.net Fri Nov 26 15:29:59 1999 Received: from metropolis.nuclecu.unam.mx (basiuk@metropolis.nuclecu.unam.mx [132.248.29.92]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA13106 for ; Fri, 26 Nov 1999 15:29:58 -0500 Received: from localhost (basiuk@localhost) by metropolis.nuclecu.unam.mx (8.8.7/8.8.7) with SMTP id NAA14446 for ; Fri, 26 Nov 1999 13:26:49 -0600 Date: Fri, 26 Nov 1999 13:26:49 -0600 (CST) From: Vladimir Basiuk To: chemistry@ccl.net Subject: TS Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, Please could you help me to clarify the following point. Is the presence of one imaginary frequency the necessary and sufficient criterion to consider the structure as TS? Thank you and best regards, Vladimir *********************************************** Dr. Vladimir Basiuk Instituto de Ciencias Nucleares Universidad Nacional Autonoma de Mexico Circuito Exterior C.U. A. Postal 70-543 04510 Mexico, D.F., MEXICO Tel: (52) 56 16 27 97 (52) 56 22 46 74 Fax: (52) 56 16 22 33 email: basiuk@nuclecu.unam.mx *********************************************** From chemistry-request@server.ccl.net Fri Nov 26 17:40:27 1999 Received: from ivory.trentu.ca (trentu.ca [192.75.12.103]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA13713 for ; Fri, 26 Nov 1999 17:40:26 -0500 Received: from el1 ([204.225.13.50]) by trentu.ca (PMDF V5.2-32 #29543) with SMTP id <01JIST36GG7K004B04@trentu.ca> for chemistry@ccl.net; Fri, 26 Nov 1999 16:33:20 EST Date: Fri, 26 Nov 1999 16:36:46 -0500 From: Errol Lewars Subject: TRANSITION STATE AND IMAGINARY..., ANSWER To: chemistry@ccl.net Message-id: <383EFD6E.7188@trentu.ca> Organization: Trent University MIME-version: 1.0 X-Mailer: Mozilla 3.01Gold (WinNT; I) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit 1999 Nov 26 Hello, Vladimir Basiuk asked: *** From: Vladimir Basiuk To: chemistry@ccl.net Dear CCLers, Please could you help me to clarify the following point. Is the presence of one imaginary frequency the necessary and sufficient criterion to consider the structure as TS? Thank you and best regards, Vladimir *** The answer is yes. A structure is a TS if and only if it has one imaginary frequency. Of course (1)this alone does not prove it is the TS you are looking for, and (2) at another level of calculation the TS may become a minimum or hilltop. E Lewars