From chemistry-request@server.ccl.net Thu Mar 21 01:36:18 2002 Received: from web13308.mail.yahoo.com ([216.136.175.44]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g2L6aIp01166 for ; Thu, 21 Mar 2002 01:36:18 -0500 Message-ID: <20020321063608.50156.qmail@web13308.mail.yahoo.com> Received: from [128.227.82.39] by web13308.mail.yahoo.com via HTTP; Wed, 20 Mar 2002 22:36:08 PST Date: Wed, 20 Mar 2002 22:36:08 -0800 (PST) From: Xiang Wang Subject: Charmm: Stack overflow error To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear CCLers: I am using Charmm c25b2 on some covarience analysis. I couldn't pass it and the error message is: CHARMM> COVARI: Covariance matrix output to unit 55 SELRPN> 3900 atoms have been selected out of 7951 SELRPN> 3900 atoms have been selected out of 7951 COVARI: Number of atoms selected for SET13900 COVARI: Number of atoms selected for SET23900 STACK> ALLSTK CALLED:: LSTUSD=******* NUMWRD=******* ***** LEVEL -4 WARNING FROM ***** ***** Stack overflow ****************************************** BOMLEV ( -2) IS REACHED - TERMINATING. WRNLEV IS 5 Execution terminated due to the detection of a fatal error. ----------------------------------------------------- It seems like that's not a hardware problem b/c I ran the program on different machines and got the same warning. Any suggestions? Thanks in advance. S. Wang __________________________________________________ Do You Yahoo!? Yahoo! Movies - coverage of the 74th Academy Awards® http://movies.yahoo.com/ From chemistry-request@server.ccl.net Thu Mar 21 13:06:41 2002 Received: from mxout2.cac.washington.edu ([140.142.33.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2LI6fp19601 for ; Thu, 21 Mar 2002 13:06:41 -0500 Received: from mailscan-out1.cac.washington.edu (mailscan-out1.cac.washington.edu [140.142.32.17]) by mxout2.cac.washington.edu (8.12.1+UW01.12/8.12.1+UW02.01) with SMTP id g2LI6VFJ014223 for ; Thu, 21 Mar 2002 10:06:35 -0800 Received: FROM mailhost1.u.washington.edu BY mailscan-out1.cac.washington.edu ; Thu Mar 21 10:06:31 2002 -0800 Received: from donald (borg.chem.washington.edu [128.95.128.134]) by mailhost1.u.washington.edu (8.12.1+UW01.12/8.12.1+UW02.01) with SMTP id g2LI6UgK007248 for ; Thu, 21 Mar 2002 10:06:30 -0800 From: "Carsten Detering" To: "ChemistryList" Subject: delphi for autodock Date: Thu, 21 Mar 2002 18:51:46 +0100 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 Dear fellow CCLers, I am interested in using Delphi (InsightII) for generating electrostatic maps for AutoDock. However, when I try to generate the grid in InsightII, I cannot change the point_spacing for the grid solution without also changing the points_per_axis. These two values seem to be somehow connected. Could anyone point out to me, how I can generate a grid that has the same size as my grid produced by autogrid (60 60 60 and 0.375 grid spacing)? And, has anyone got a script that converts Delphi grids into autodock grids? THis question was asked before by someone else, but I couldn't find an answer. Thanks a lot in advance, Carsten ------------------------ Carsten Detering, Ph.D. University of Washington Seattle, WA 98195 Phone: 206 543 5081 email: detering@u.washington.edu From chemistry-request@server.ccl.net Thu Mar 21 15:55:16 2002 Received: from ned1.sims.nrc.ca ([132.246.108.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2LKtGp23151 for ; Thu, 21 Mar 2002 15:55:16 -0500 Received: from fm6 (fm6.sims.nrc.ca [132.246.100.170]) by ned1.sims.nrc.ca (8.8.8/8.8.8) with SMTP id PAA27697 for ; Thu, 21 Mar 2002 15:55:09 -0500 (EST) From: "Hongbin Du" To: Subject: Mulliken population analysis Date: Thu, 21 Mar 2002 15:54:06 -0500 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" 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 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 Dear CCLers, It seems to me that Gaussian program does not provide a complete Mulliken population analysis which gives the composition of the MOs in terms of various AOs. Could someone please recommand any program that can? Thanks in advance. Hongbin Du, PhD Steacie Institute for Molecular Sciences National Research Council Ottawa, Ontario K1A 0R6, Canada From chemistry-request@server.ccl.net Thu Mar 21 18:50:55 2002 Received: from carbon.chem.ucla.edu ([128.97.35.55]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2LNosp27889 for ; Thu, 21 Mar 2002 18:50:54 -0500 Received: from silicon.chem.ucla.edu (silicon.chem.ucla.edu [169.232.135.10]) by carbon.chem.ucla.edu (8.11.4/8.11.4) with ESMTP id g2LNom407932; Thu, 21 Mar 2002 15:50:48 -0800 (PST) Received: from Laurence.mbi.ucla.edu (pc-ll.chem.ucla.edu [128.97.35.245]) by silicon.chem.ucla.edu (8.11.1/8.11.1) with ESMTP id g2LNomQ22638; Thu, 21 Mar 2002 15:50:48 -0800 (PST) Message-Id: <5.1.0.14.2.20020321154718.02f97aa0@mbi.ucla.edu> X-Sender: lavelle@mbi.ucla.edu X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Thu, 21 Mar 2002 15:50:43 -0800 To: CCL From: Laurence Lavelle Subject: Chem 3D Ultra 7.0 as a Gaussian interface. Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed I tried using Chem 3D version 5 as a Gaussian interface some time back but it was full of bugs. Anyone having successful use of Chem 3D Ultra 7.0 as a Gaussian interface ? In particular for pdb files ? Thanks, Laurence From chemistry-request@server.ccl.net Thu Mar 21 21:55:46 2002 Received: from gandalf.cber.nih.gov ([128.231.52.5]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2M2tkp01905 for ; Thu, 21 Mar 2002 21:55:46 -0500 Received: from localhost (rvenable@localhost) by gandalf.cber.nih.gov (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id VAA16938; Thu, 21 Mar 2002 21:50:10 -0500 (EST) Date: Thu, 21 Mar 2002 21:50:10 -0500 From: Rick Venable To: CCL cc: "Dr. Richard L. Wood" , Jim Phillips Subject: Re: CCL:trajectory file conversion (update) In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII The f.p. difference I mentioned for CHARMM vs. CHARMm would seem to be historical; both use double precision (REAL*8) for coordinate and other f.p. numbers, and have for some time (years). I have not yet determined why I had problems with flipdcd previously-- but I plan to try again > from source (rather than pre-compiled Linux binary). I should also note that the trajectory transfer format (produced by DYNA FORMAT, converted back to binary via DYNA UNFORMAT) was changed at ca. CHARMM v. 27, in a way that lost backwards compatibility. It is strongly recommended that the same CHARMM version be used on both machine types in order to accomplish trajectory transfer via this mechanism. Finally, I should note that while CHARMM is not free, it is available as academically licensed source for a modest fee, a well crafted letter, and a bit of patience. Here's the information from the Karplus group: ----------------------------------------------------- We distribute the source code of the CHARMM program with documentation to individual academic research groups for a $600 licensing fee. CHARMM runs on a variety of UNIX workstations, including the SG Indigo machines. No graphics are necessary. The present version of the program being distributed is C28. The license is issued to the head of a laboratory or research group. Please send a letter with the full name and title of the professor in charge of your group and formal mailing address. Describe briefly the kind of research for which you intend to use the CHARMM program and the computers you will be using. The letter should be addressed to: The CHARMM Development Project Professor Martin Karplus Department of Chemistry & Chemical Biology 12 Oxford Street Harvard University Cambridge, Massachusetts 02138 ----------------------------------------------------- =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= 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@nih.gov ALT email: rvenable@speakeasy.org =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=