From chemistry-request@server.ccl.net Wed Dec 4 04:44:00 2002 Received: from gwia.kvl.dk ([130.225.43.254]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gB49hxA23418 for ; Wed, 4 Dec 2002 04:43:59 -0500 Received: from kvl.dk (pwt.kemi.kvl.dk [130.225.43.124]) by gwia.kvl.dk; Wed, 04 Dec 2002 10:43:29 +0100 Sender: pwt@ccl.net Message-ID: <3DEDCE82.7AD97AAE@kvl.dk> Date: Wed, 04 Dec 2002 10:44:34 +0100 From: Peter Waaben Thulstrup Organization: Royal Veterinary and Agricultural University X-Mailer: Mozilla 4.79 [en] (X11; U; Linux 2.4.18-4GB i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: g98 chkmove error with large checkpoint files Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL, I occasionally have trouble with chkmove, when I want to convert large checkpoint files. The error occurs in cases where the job has terminated normally, and it is apparently related to the file size. An example: pwt $ ls -l cc_pVTZ_td.chk -rw-r--r-- 1 kvlpwt kvl 611123200 Nov 27 10:09 cc_pVTZ_td.chk ~/ea/cc_pVTZ/td pwt $ chkmove f cc_pVTZ_td.chk cc_pVTZ_td.xfr File 635 LenFil= 29348210 but MDV= 6291456. Error termination in NtrErr: NtrErr called from Fatal. Segmentation Fault ~/ea/cc_pVTZ/td I would really appreciate any advice which will help me convert the file. Thanks, Peter -- Peter W. Thulstrup Chemistry Department / Royal Veterinary and Agricultural University Thorvaldsensvej 40 / DK-1871 Frederiksberg C / Denmark Phone (Chemistry Dep't): +45 35282400 / Fax: +45 35282398 Phone (Office - direct): +45 35282464 / E-mail: pwt@kvl.dk From chemistry-request@server.ccl.net Wed Dec 4 06:51:55 2002 Received: from anor.ics.muni.cz ([147.251.4.35]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gB4BptA26945 for ; Wed, 4 Dec 2002 06:51:55 -0500 Received: from bilbo.chemi.muni.cz (bilbo.chemi.muni.cz [147.251.28.2]) by anor.ics.muni.cz (8.12.1/8.12.1) with ESMTP id gB4BpnRF030266 for ; Wed, 4 Dec 2002 12:51:49 +0100 Received: from chemi.muni.cz (snail.chemi.muni.cz [147.251.28.27]) by bilbo.chemi.muni.cz (8.9.3/8.8.5) with ESMTP id MAA02355 for ; Wed, 4 Dec 2002 12:51:49 +0100 (MET) Message-ID: <3DEDE228.5020908@chemi.muni.cz> Date: Wed, 04 Dec 2002 12:08:24 +0100 From: Lubos Vrbka Reply-To: shnek@chemi.muni.cz Organization: National Centre for Biomolecular Research User-Agent: Mozilla/5.0 (X11; U; NetBSD i386; en-US; rv:1.0.0) Gecko/20020925 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry@ccl.net Subject: temperature control in AMBER / NAMD Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Muni-Virus-Test: Clean dear CCLers, i'm trying to "translate" AMBER input to NAMD, but i experienced following "problem": tempi = 300.0, temp0 = 300.0, ntt = 1, tautp = 0.5, can be "translated" into NAMD as temperature 300 rescaletemp 300 rescalefreq 500 or using tcouple, tcoupletemp, tcouplefile and tcouplecol parameters. is the former "translation" sufficient and will it do what i expect (i.e. hold the temperature at 300K using rescaling forces to 300K every 500th step)? it seems to me that NAMD doesn't support berendsen temperature coupling algorithm used in AMBER (ntt = 1), just berendsen pressure bath coupling, that is not useful for me at this time since i do just vacuum simulation. in case i'll use tcouple on tcoupletemp 300 tcouplefile name.pdb tcouplecol b what value should i set as the beta-factor in the pdb file? i'm not experienced with this, i'd expect using value 1 for all atoms should be ok. could anyone help me, please? TIA l.vrbka -- ################################################# Lubos Vrbka National Centre for Biomolecular Research Masaryk university, Brno, Czech Republic shnek@chemi.muni.cz http://www.chemi.muni.cz/~shnek tel. +420 5 4112 9508 ################################################# From chemistry-request@server.ccl.net Tue Dec 3 18:20:16 2002 Received: from ra.abo.fi ([130.232.213.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gB3NKGO27855 for ; Tue, 3 Dec 2002 18:20:16 -0500 Received: from tuxedo.abo.fi (IDENT:root@tuxedo.abo.fi [130.232.213.61]) by ra.abo.fi (8.10.1/8.10.1) with ESMTP id gB3NKFL28473 for ; Wed, 4 Dec 2002 01:20:15 +0200 (EET) From: Mikko Huhtala BKF Received: (from nobody@localhost) by tuxedo.abo.fi (8.9.3/8.8.7) id BAA04253 for chemistry@ccl.net; Wed, 4 Dec 2002 01:20:15 +0200 X-Authentication-Warning: tuxedo.abo.fi: nobody set sender to mhuhtala@abo.fi using -f To: chemistry@ccl.net Subject: AutoDock 3: multiple ligands in one dpf? Message-ID: <1038957615.3ded3c2f4e39c@webmail.abo.fi> Date: Wed, 04 Dec 2002 01:20:15 +0200 (EET) MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: IMP/PHP IMAP webmail program 2.2.6-aau3 X-Mailer: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.0.1) Gecko/20021026 X-Originating-IP: 80.74.210.60 Has anyone tried using multiple 'move' commands in one AutoDock 3.0.5 input dpf file? Is there a working example of a multi-'move' dpf file? Was the program ever meant to dock more than one ligand per run? In the dpf I tried [ ... the usual map etc. parameter lines... ] move lig1.pdbq about 2.8527 3.4304 0.0000 ndihe 1 tran0 random quat0 random dihe0 random ga_run 10 move lig2.pdbq about 2.7408 3.3823 0.0397 ndihe 5 tran0 random quat0 random dihe0 random ga_run 10 [ and so on ] Docking many ligands this way has the performance advantage that the map files are only read into memory once. The autodock3 program accepts multiple 'move' commands in one dpf file and does dock multiple ligands, but the output file (dlg) lists errors on construction of the ligand internal non-bonded interactions for all but the first ligand with rotatable bonds. If the same ligands are docked one by one (one dpf file with one 'move' for each), there are no errors. It seems that the array that contains the non-bonded interacting atoms (nbmatrix_binary in weedbond.cc source file) is not cleared between the ligands. When a new ligand is read in, the computation of non-bonded interactions fails because the table is corrupt and hence ligand internal energies are wrong. The cluster analysis fails, too, since the conformation set is also not cleared between ligands, but I can do without cluster analysis. Mikko Huhtala From chemistry-request@server.ccl.net Tue Dec 3 18:57:44 2002 Received: from web12607.mail.yahoo.com ([216.136.173.230]) by server.ccl.net (8.11.6/8.11.0) with SMTP id gB3NviO28666 for ; Tue, 3 Dec 2002 18:57:44 -0500 Message-ID: <20021203235740.4016.qmail@web12607.mail.yahoo.com> Received: from [143.111.14.169] by web12607.mail.yahoo.com via HTTP; Tue, 03 Dec 2002 15:57:40 PST Date: Tue, 3 Dec 2002 15:57:40 -0800 (PST) From: Mao Xiang Subject: mosflm for windows To: CHEMISTRY@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hello, everyone: I wonder if someone have the binary program of MOSFLM compiled under windowNT system. Thanks in advance. Regards, Xiang Mao __________________________________________________ Do you Yahoo!? Yahoo! Mail Plus - Powerful. Affordable. Sign up now. http://mailplus.yahoo.com From chemistry-request@server.ccl.net Wed Dec 4 05:35:57 2002 Received: from zeta.qmw.ac.uk ([138.37.6.6]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gB4AZuA24916 for ; Wed, 4 Dec 2002 05:35:57 -0500 Received: from smtp.qmul.ac.uk ([138.37.6.40]) by zeta.qmw.ac.uk with esmtp (Exim 3.32 #1) id 18JWsZ-00024J-00; Wed, 04 Dec 2002 10:35:43 +0000 Received: from debye.chem.qmw.ac.uk ([138.37.52.177] helo=qmul.ac.uk) by smtp.qmul.ac.uk with esmtp (Exim 3.35 #5) id 18JWsZ-0000mU-00; Wed, 04 Dec 2002 10:35:43 +0000 Sender: pascal@ccl.net Message-ID: <3DEDDA83.878CA67B@qmul.ac.uk> Date: Wed, 04 Dec 2002 10:35:47 +0000 From: Pascal Boulet Organization: Queen Mary, University of London X-Mailer: Mozilla 4.79C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: Vlad.Cojocaru@mpi-bpc.mpg.de, pgannett@hsc.wvu.edu, CCL Subject: freeware for RNA modeling on Linux Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit An alternative to NAMD is LAMMPS. http://www.cs.sandia.gov/~sjplimp/lammps.html Pascal -- Dr. Pascal Boulet Queen Mary, University of London Centre for Computational Science Department of Chemistry Mile End Road London, E1 4NS UK Phone: (+44) (0)20 7882 7759 fax: (+44) (0)20 7882 7794 From chemistry-request@server.ccl.net Wed Dec 4 11:39:41 2002 Received: from mta2n.bluewin.ch ([195.186.4.220]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gB4GdeA03423 for ; Wed, 4 Dec 2002 11:39:40 -0500 Received: from bluewin.ch (62.202.110.113) by mta2n.bluewin.ch (Bluewin AG 6.5.032) id 3DE760510008CE76; Wed, 4 Dec 2002 17:39:27 +0100 Message-ID: <3DEDF392.AFC0715F@bluewin.ch> Date: Wed, 04 Dec 2002 13:22:42 +0100 From: Andras Borosy Reply-To: borosy@bluewin.ch X-Mailer: Mozilla 4.79C-CCK-MCD bwch-cd-en-4 (Macintosh; U; PPC) X-Accept-Language: en,de-CH,fr-CH,it MIME-Version: 1.0 To: David Clark CC: "'chemistry@ccl.net'" Subject: Re: CCL:Tools for HTS Data Analysis References: <2A5044E3B5F36440814C888668E9D6A564E9AF@pallas_ex003.pallas_uk> Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit Dear Dr. Clark, > > Does anyone have any experience that they would be willing to share of tools > for HTS data analysis, particularly those that aim to help in the analysis > of (qualitative) SAR? Generally the commercial chemoinformatical appliactions (e.g. Sybyl, Discovery Studio, MOE etc) have moduls for HTS data analysis. As a special tool you I suggest Bioreason`s Classpharmer (www.bioreason.com). Best regards, Andras Borosy Ph.D. computational chemist > > > I will summarise any responses for the list. > > Many thanks > > David E. Clark, PhD. > Project Leader (Computer-Aided Drug Design) > Argenta Discovery Ltd. > 8/9 Spire Green Centre > Harlow > Essex > CM19 5TR > United Kingdom > Telephone Direct: +44 (0) 1279 645 611 > Telephone Switchboard: +44 (0) 1279 645 645 > Fax: +44 (0) 1279 645 646 > E-mail: david.clark@argentadiscovery.com > Web site: www.argentadiscovery.com > Legal Notice > Unless expressly stated otherwise, this message is confidential and may be > privileged. It is intended for the addressee(s) only. Access to this e-mail > by anyone else is unauthorized. If you are not an addressee, any disclosure > or copying of the contents of this e-mail or any action taken (or not taken) > > in reliance on it is unauthorised and may be unlawful. If you are not an > addressee, please inform the sender immediately. > Further, Argenta Discovery makes every effort to keep its network free from > viruses including the scanning of incoming and outgoing mail. However, you > do need to check this e-mail and any attachments to it for viruses, as > Argenta Discovery can take no responsibility for any computer virus that > might be transferred by way of this e-mail. > Argenta Discovery Limited is registered in England: No. 3671653 with its > registered office at 8/9 Spire Green Centre, Flex Meadow, Harlow, Essex, > CM19 5TR, UK > VAT registration number GB 736 3943 12 > > -= 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 Wed Dec 4 09:57:27 2002 Received: from postmark.nist.gov ([129.6.16.93]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gB4EvRA32734 for ; Wed, 4 Dec 2002 09:57:27 -0500 Received: from SILYL.nist.gov (silyl.nist.gov [129.6.194.163]) by postmark.nist.gov (8.12.5/8.12.5) with ESMTP id gB4EvFVN002966 for ; Wed, 4 Dec 2002 09:57:16 -0500 (EST) Message-Id: <5.0.0.25.2.20021204094800.02a340f8@mailserver.nist.gov> X-Sender: rdj3@mailserver.nist.gov X-Mailer: QUALCOMM Windows Eudora Version 5.0 Date: Wed, 04 Dec 2002 09:56:31 -0500 To: CHEMISTRY@ccl.net From: Russ Johnson Subject: rotational barriers Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Hello, There is a little bit of data on rotational barriers in the NIST Computational Chemistry Comparison and Benchmark database. http://srdata.nist.gov/cccbdb It does contains an experimental number and a few calculated (QM) scans of the methyl torsion for propylene oxide (see section IV.A.5) The experimental reference is: JD Swalen, DR Herschbach, "Internal barrier of propylene oxide from the microwave spectrum. I" J. Chem. Phys. 27(1), 100, 1957 Hope this helps, Russ Johnson Dr. Russell D. Johnson III Research Chemist National Institute of Standards and Technology Computational Chemistry Group 100 Bureau Drive, Stop 8380 Gaithersburg, MD 20899-8380 voice 301+975-2513 fax 301+869-4020 email: russell.johnson@nist.gov From chemistry-request@server.ccl.net Wed Dec 4 11:39:41 2002 Received: from mta2n.bluewin.ch ([195.186.4.220]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gB4GdeA03424 for ; Wed, 4 Dec 2002 11:39:40 -0500 Received: from bluewin.ch (62.202.110.113) by mta2n.bluewin.ch (Bluewin AG 6.5.032) id 3DE760510008CE6F; Wed, 4 Dec 2002 17:39:24 +0100 Message-ID: <3DEDF36B.40530B19@bluewin.ch> Date: Wed, 04 Dec 2002 13:22:04 +0100 From: Andras Borosy Reply-To: borosy@bluewin.ch X-Mailer: Mozilla 4.79C-CCK-MCD bwch-cd-en-4 (Macintosh; U; PPC) X-Accept-Language: en,de-CH,fr-CH,it MIME-Version: 1.0 To: james.metz@abbott.com CC: chemistry@ccl.net Subject: Re: CCL:Natural products catalog in SDF format References: Content-Type: multipart/alternative; boundary="------------3275544E14BFFB32F5673A79" --------------3275544E14BFFB32F5673A79 Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit Dear Dr. Metz, The following companies offer their natural products libraries in sdf format, as well: Analyticon Biotechnologies AG 1554 Am Muehlenberg 10 , D-35104 Lichtenfels, Germany 49 (0) 6454 7991 - 0 +49 (0) 6454 7991 - 30 http://www.combiscreen.de Bionet Research 34693 Unit 2, Highfield Road, Camelford, PL32 9QZ, UK 01840 212171 01840 213712 bionet@keyorganics.ltd.uk http://www.bionetresearch.co.uk Cerep 197260 128, Rue Danton, BP 50601, 92506 Rueil-Malmaison, FRANCE 33 (0)1 55 94 84 00 +33 (0)1 55 94 84 10 j.windsor@cerep.fr www.cerep.com cerep IF LAB 373113 P.O. Box 536, 01004 Kiev, Ukraine + 38 (044) 574-1446 + 38 (044) 574-1417 iflab@iflab.kiev.ua http://www.iflab.kiev.ua/ InterBioScreen Ltd 154161 PO Box 218, 121019 Moscow, Russia. 0r Room 420, Institutski Prospekt 8, Chernogolovka, 142432, Russia 00 7 095 913 2319 00 7 095 913 2114 screen@ibscreen.chg.ru http://www.ibscreen.com Nanoscale Combinatorial Synthesis Inc 65328 3603 Haven Ave. Suite E, Menlo Park, CA 94025 USA 1 650-299-1854 1 650-299-1874 info@nanosyn.com http://www.nanosyn.com Pharmacore 41186 4170 Mendenhall Oaks Pkwy. Ste. 140 High Point, NC 27265-8034, USA 1 (866) 841-5250 1 (336) 841-5350 info@pharmacore.com http://www.pharmacore.com SPECS and BioSPECS B.V. 99296 Fleminglaan 16, 2289 CP Rijswijk, The Netherlands 31 70 319 0038 31 70 319 0011 jan.schultz@specs.net http://www.specs.net TimTec Inc 371519 100 Interchange Boulevard, Newark, DE 19711, USA 302-292-8500 302-292-8520 info@timtec.net http://www.timtec.net/ Best regards, Andras Borosy Ph.D. computational chemist > > CCL, > > I am looking for catalogs of isolated, available natural > products which are in SDF format. Does anyone know of sources > for this information? > > Please note that I am not interested in catalogs of compounds > which would typically be included in the Available > Chemicals Directory (ACD), even if ACD is (often) behind current > inventory. > > Thank you, > Jim Metz > > > > James T. Metz, Ph.D. > Research Investigator Chemist > > GPRD R46Y AP10-2 > Abbott Laboratories > 100 Abbott Park Road > Abbott Park, IL 60064-6100 > U.S.A. > > Office (847) 936 - 0441 > FAX (847) 935 - 0548 > > james.metz@abbott.com --------------3275544E14BFFB32F5673A79 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Dr. Metz,

The following companies offer their natural products libraries in sdf format, as well:

Analyticon Biotechnologies AG 1554 Am Muehlenberg 10 , D-35104 Lichtenfels, Germany 49 (0) 6454 7991 - 0 +49 (0) 6454 7991 - 30  http://www.combiscreen.de

Bionet Research 34693 Unit 2, Highfield Road, Camelford, PL32 9QZ, UK 01840 212171 01840 213712 bionet@keyorganics.ltd.uk http://www.bionetresearch.co.uk

Cerep 197260 128, Rue Danton, BP 50601, 92506 Rueil-Malmaison, FRANCE 33 (0)1 55 94 84 00 +33 (0)1 55 94 84 10 j.windsor@cerep.fr www.cerep.com cerep

IF LAB 373113 P.O. Box 536, 01004 Kiev, Ukraine  + 38 (044) 574-1446  + 38 (044) 574-1417  iflab@iflab.kiev.ua http://www.iflab.kiev.ua/

InterBioScreen Ltd 154161 PO Box 218, 121019 Moscow, Russia. 0r Room 420, Institutski Prospekt 8, Chernogolovka, 142432, Russia 00 7 095 913 2319 00 7 095 913 2114 screen@ibscreen.chg.ru http://www.ibscreen.com

Nanoscale Combinatorial Synthesis Inc 65328 3603 Haven Ave. Suite E, Menlo Park, CA 94025 USA  1 650-299-1854 1 650-299-1874 info@nanosyn.com http://www.nanosyn.com

Pharmacore 41186 4170 Mendenhall Oaks Pkwy. Ste. 140 High Point, NC 27265-8034, USA 1 (866) 841-5250 1 (336) 841-5350 info@pharmacore.com http://www.pharmacore.com
SPECS and BioSPECS B.V. 99296 Fleminglaan 16, 2289 CP Rijswijk, The Netherlands 31 70 319 0038 31 70 319 0011 jan.schultz@specs.net http://www.specs.net

TimTec Inc 371519 100 Interchange Boulevard, Newark, DE 19711, USA 302-292-8500 302-292-8520 info@timtec.net http://www.timtec.net/

Best regards,

Andras Borosy
Ph.D. computational chemist
 

 
CCL,

        I am looking for catalogs of isolated, available natural products which are in SDF format.  Does anyone know of sources
for this information?

        Please note that I am not interested in catalogs of compounds which would typically be included in the Available
Chemicals Directory (ACD), even if ACD is (often) behind current inventory.

        Thank you,
        Jim Metz
 
 

James T. Metz, Ph.D.
Research Investigator Chemist

GPRD R46Y AP10-2
Abbott Laboratories
100 Abbott Park Road
Abbott Park, IL  60064-6100
U.S.A.

Office (847) 936 - 0441
FAX    (847) 935 - 0548

james.metz@abbott.com

--------------3275544E14BFFB32F5673A79-- From chemistry-request@server.ccl.net Wed Dec 4 17:25:19 2002 Received: from cornell.edu ([132.236.56.6]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gB4MPJA12900 for ; Wed, 4 Dec 2002 17:25:19 -0500 Received: from cornell.edu (lock.lassp.cornell.edu [128.84.241.198]) by cornell.edu (8.9.3/8.9.3) with ESMTP id RAA08788 for ; Wed, 4 Dec 2002 17:25:18 -0500 (EST) Sender: cc236@cornell.edu Message-ID: <3DEE80CE.EAEA50B3@cornell.edu> Date: Wed, 04 Dec 2002 17:25:18 -0500 From: Connie Chang X-Mailer: Mozilla 4.79 [en] (X11; U; Linux 2.4.18-10smp i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Gaussian98W - Hessian matrix in archive & frequencies? Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi -- I was wondering if you could help me out with a problem I'm stuck with. I got the Hessian matrix (which was in lower triangular form) from the archive entry at the end of the output file and I try to diagonalize it to find the eigenvalues. But the eigenvalues I get don't match the eigenvalue frequencies Gaussian gives me in the output file! What step am I missing? It can't be because of mass-weighting because my molecule is composed of only the element carbon; so even if my eigenvalues are off when I diagonalize the Hessian, shouldn't they just be off by a constant? But the differences between the frequencies I get by diagonalizing the Hessian and the frequencies Gaussian outputs don't just differ by a multiplicative constant... Thanks, Connie From chemistry-request@server.ccl.net Wed Dec 4 18:24:02 2002 Received: from cornell.edu ([132.236.56.6]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gB4NO2A14528 for ; Wed, 4 Dec 2002 18:24:02 -0500 Received: from cornell.edu (lock.lassp.cornell.edu [128.84.241.198]) by cornell.edu (8.9.3/8.9.3) with ESMTP id SAA22247 for ; Wed, 4 Dec 2002 18:24:01 -0500 (EST) Sender: cc236@cornell.edu Message-ID: <3DEE8E91.6A5A70BC@cornell.edu> Date: Wed, 04 Dec 2002 18:24:01 -0500 From: Connie Chang X-Mailer: Mozilla 4.79 [en] (X11; U; Linux 2.4.18-10smp i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: please disregard my recent question Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi -- I'm very sorry. Re: the Hessian matrix and the eigenvalue frequencies in Gaussian98W. I just realized that in the frequency check I did, I forgot to take the square root of the eigenvalue. Thanks.... Connie From chemistry-request@server.ccl.net Wed Dec 4 13:04:23 2002 Received: from ra.abo.fi ([130.232.213.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gB4I4NA06033 for ; Wed, 4 Dec 2002 13:04:23 -0500 Received: from urquell.abo.fi.abo.fi (urquell.abo.fi [130.232.210.248]) by ra.abo.fi (8.10.1/8.10.1) with ESMTP id gB4I4Cf19195; Wed, 4 Dec 2002 20:04:18 +0200 (EET) From: Mikko Huhtala MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Message-ID: <15854.17308.912376.956625@urquell.abo.fi> Date: Wed, 4 Dec 2002 20:04:12 +0200 To: CC: chemistry@ccl.net Subject: Re: CCL:AutoDock 3: multiple ligands in one dpf? In-Reply-To: References: <1038957615.3ded3c2f4e39c@webmail.abo.fi> X-Mailer: VM 7.03 under Emacs 21.2.1 csaba@ovrisc.mdche.u-szeged.hu writes: > > > Was the program ever meant to dock more than one ligand per run? > > In the source there are some definitions of 'maximum number of ligands' or > something like this... Maybe, the authors wanted to make it for multiple > ligands, but then changed their mind... > Best, > Csaba That's the impression I got from the source, too. I managed to modify autodock3 to do multiple ligands, though. The culprits seem to be the arrays Nnbonds and nonbondlist, which are reserved and initialized at the beginning of main() and then passed to readPDBQ(), which passes the references to other functions. The arrays are never re-initialized, even if new ligands are read in. There are loops to initialize various arrays with zeroes in the beginning of main(). I cut and pasted selected bits of this code into the 'case DPF_MOVE' block, so the arrays are initialized every time a new ligand is read in. I do not want to post the code as I am not sure if it always produces correct results, but at least after very quick testing the output seems to be consistent with single-'move' dpf runs. Another mistake I had made before was not to give the 'torsdof' command for every ligand that is read in and hence my torsional energies were wrong. Mikko Huhtala From chemistry-request@server.ccl.net Wed Dec 4 14:47:54 2002 Received: from mtiwmhc11.worldnet.att.net ([204.127.131.115]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gB4JlsA08763 for ; Wed, 4 Dec 2002 14:47:54 -0500 Received: from dopetec ([138.23.156.82]) by mtiwmhc11.worldnet.att.net (InterMail vM.5.01.05.13 201-253-122-126-113-20020917) with ESMTP id <20021204194753.ZEIP20860.mtiwmhc11.worldnet.att.net@dopetec> for ; Wed, 4 Dec 2002 19:47:53 +0000 From: "Donald Keidel" To: Subject: Gaussian 98 on AMD Cluster using something other than Linda Date: Wed, 4 Dec 2002 11:47:53 -0800 Message-ID: <001801c29bce$094cedc0$529c178a@dopetec> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0019_01C29B8A.FB29ADC0" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.3416 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 This is a multi-part message in MIME format. ------=_NextPart_000_0019_01C29B8A.FB29ADC0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Hello all, Has anyone been successful in setting up a Linux Cluster that runs Gaussian 98 in parallel using software other than Linda? I ask this since our lab is not that wealthy and Linda + Gaussian is a little expensive. Thank you. 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 dkeidel397@att.net webpage: www.biochemistry.ucr.edu/gru/gradstudents/don_keidel/index.htm ------=_NextPart_000_0019_01C29B8A.FB29ADC0 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Hello all,

 

Has anyone been successful in setting up a Linux = Cluster that runs Gaussian 98 in parallel using software other than Linda?  = I ask this since our lab is not that wealthy and Linda + Gaussian is a little = expensive.  Thank you.

 

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
dkeidel397@att.net
webpage: www.biochemistry.ucr.edu/gru/gradstudents/don_keidel/index.htm<= /span>

 

 

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