From chemistry-request@www.ccl.net Wed Nov 18 07:51:06 1998 Received: from hartree.chem.kuleuven.ac.be (hartree.quantchem.kuleuven.ac.be [134.58.49.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id HAA06131 Wed, 18 Nov 1998 07:50:22 -0500 (EST) Received: from localhost (steven@localhost) by hartree.chem.kuleuven.ac.be (8.9.0/8.9.0) with ESMTP id NAA47040 for ; Wed, 18 Nov 1998 13:49:45 +0100 Date: Wed, 18 Nov 1998 13:49:44 +0100 (NFT) From: Steven Creve To: Computational Chemistry List Subject: CCL:DFT: local / non-local Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi. two questions concerning DFT functionals: 1) what are the *exact* definitions of local vs. non-local? 2) is the LYP correlation functional, which incorporates gradient corrections, local or non-local? Steven -------------------------------------------------------------------------- Steven Creve steven.creve@chem.kuleuven.ac.be Labo Quantumchemie Celestijnenlaan 200F 3001-HEVERLEE tel: (32) (16) 32 73 93 BELGIUM fax: (32) (16) 32 79 92 From chemistry-request@www.ccl.net Wed Nov 18 09:04:50 1998 Received: from romeo.ic.ac.uk (romeo.ic.ac.uk [155.198.5.9]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id JAA06626 Wed, 18 Nov 1998 09:04:40 -0500 (EST) Received: from oban.cc.ic.ac.uk [155.198.5.28] by romeo.ic.ac.uk with smtp (Exim 1.62 #1) id 0zg8Dj-0004F9-00; Wed, 18 Nov 1998 14:04:35 +0000 Received: from mtcmsag1.mt.ic.ac.uk ([155.198.96.22] helo=mtcmsa.mt.ic.ac.uk ident=root) by oban.cc.ic.ac.uk with smtp (Exim 1.90 #1) for CHEMISTRY@www.ccl.net id 0zg8DT-0007eh-00; Wed, 18 Nov 1998 14:04:19 +0000 Received: from foxymulder.mt.it.ac.uk (mt6) by mtcmsa.mt.ic.ac.uk (5.x/4.1) id AA29054; Wed, 18 Nov 1998 14:04:17 GMT Message-Id: <4.1.19981118140042.00ad4810@icex5.cc.ic.ac.uk> X-Sender: ic\seth\s.hogg@icex5.cc.ic.ac.uk X-Mailer: QUALCOMM Windows Eudora Pro Version 4.1 Date: Wed, 18 Nov 1998 14:03:16 +0000 To: CHEMISTRY@www.ccl.net From: Simon Hogg Subject: Huzinaga vs. Pople? Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" I was given a book by Huzinaga (Gaussian Basis Sets) and was looking through, comparing a couple of them to Pople's basis sets. There appears to be slight differences (maybe 3rd or 4th significant figure) but they are more-or-less the same. Can anyone say why they are different, and which is 'better' (yes, I know Pople is a Nobel Laureate, and Huzinaga isn't, but ...) -- Simon Hogg, Imperial College, London, UK Tel. +44 171 589 5111 ext. 56721 Fax. +44 171 584 3194 Email: s.hogg@ic.ac.uk Glass-List: glass-list@ic.ac.uk PGP: Key ID 0x4C048B49 Send "get public key" as subject for key FingerPrint B9C7 4E40 C73D 0E15 15E0 D6C6 79C4 AB59 4C04 8B49 From chemistry-request@www.ccl.net Wed Nov 18 09:10:37 1998 Received: from toronto.acdlabs.com (root@toronto.acdlabs.com [207.176.233.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA06688 Wed, 18 Nov 1998 09:10:36 -0500 (EST) Received: from michael.acdlabs.com (michael.acdlabs.com [207.176.233.24]) by toronto.acdlabs.com (8.9.0/8.9.0) with SMTP id JAA25107; Wed, 18 Nov 1998 09:10:31 -0500 (EST) Message-ID: <001c01be12f4$bedb0ee0$18e9b0cf@michael.acdlabs.com> From: "Michael McBrien" To: Cc: Subject: Re: CCL:CHARMm questions Date: Wed, 18 Nov 1998 08:09:15 -0500 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 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 I have found one CHARMm discussion group. The address is: http://alchemy.yonsei.ac.kr/~lsk/list.c.html#CHARMM-BBS I hope that this is of help to you. Mike. ------------------------------------------------------------------------- Michael McBrien M.Sc. Technical Support Specialist Advanced Chemistry Development 133 Richmond St., W., Suite 605 Toronto, Ontario, Canada M5H 2L3 416-368-3435 The most chemically intelligent database software for chemists has just arrived! Introducing Advanced/ChemFolder, the newest star in the expanding Advanced Chemistry Development universe. ChemFolder integrates its renowned ChemSketch interface with a powerful and flexible database management system. Organizing your information has never been so easy! See www.acdlabs.com for further details. ------------------------------------------------------------------------- -----Original Message----- From: MARYJO@neu.edu To: CHEMISTRY@www.ccl.net Date: Tuesday, November 17, 1998 5:06 PM Subject: CCL:CHARMm questions >Hello. I have a student who is doing dynamics calculations >on a macromolecule. I have not used the CHARMm program much, >and have some questions: > >1) Is there a listserv for CHARMm users? > >2) Troubleshooting strategies - when the calculation crashes and you >receive a warning - what is the best way to troubleshoot. (e.g. He >is getting a warning saying Level -2 warning - Energy change tolerance >exceeded") I am not sure how to advise him to play with the options >to get around such problems - can anybody make suggestions about the >best place to learn strategy for using the program? > >Thanks very much. > >Mary j.o. > >-------This is added Automatically by the Software-------- >-- Original Sender Envelope Address: chemistry-request@www.ccl.net >-- Original Sender From: Address: MARYJO@neu.edu >CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator >MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 >Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > > From chemistry-request@www.ccl.net Wed Nov 18 09:48:21 1998 Received: from e45.it.ki.se (e45.it.ki.se [130.237.98.100]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA07668 Wed, 18 Nov 1998 09:48:19 -0500 (EST) Received: from thon.csb.ki.se (thon.csb.ki.se [130.237.204.199]) by e45.it.ki.se (8.7.5/8.7.3) with SMTP id PAA19752; Wed, 18 Nov 1998 15:42:36 +0100 (MET) Received: from whale.csb.ki.se by thon.csb.ki.se (4.1/SMI-4.1) id AA18240; Wed, 18 Nov 98 15:58:06 +0100 Received: from sill.csb.ki.se by whale.csb.ki.se (5.65v3.2/1.1.10.5/03Feb98-0237PM) id AA09269; Wed, 18 Nov 1998 15:49:08 +0100 Message-Id: <3652DE56.A297B669@csb.ki.se> Date: Wed, 18 Nov 1998 15:48:54 +0100 From: Yun Tang Reply-To: Yun.Tang@csb.ki.se Organization: Karolinska Institute X-Mailer: Mozilla 4.5 [en] (Win95; I) X-Accept-Language: en,zh Mime-Version: 1.0 To: maryjo@neu.edu, chemistry@www.ccl.net Subject: Re: CCL:CHARMm questions References: <001c01be12f4$bedb0ee0$18e9b0cf@michael.acdlabs.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, I found the following CHARMM-BBS which may be helpful to you: CHARMM Users Discussions (charmm-bbs) List management address: majordomo@csir.org List manager: majordomo Posting address: charmm-bbs@csir.org Yun -- ************************************ Yun TANG, Ph.D. Center for Structural Biochemistry Department of Biosciences at Novum Karolinska Institute S-141 57 Huddinge Sweden ************************************ From chemistry-request@www.ccl.net Wed Nov 18 10:36:05 1998 Received: from hartree.chem.kuleuven.ac.be (hartree.quantchem.kuleuven.ac.be [134.58.49.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA15413 Wed, 18 Nov 1998 10:36:02 -0500 (EST) Received: from localhost (steven@localhost) by hartree.chem.kuleuven.ac.be (8.9.0/8.9.0) with ESMTP id QAA28334 for ; Wed, 18 Nov 1998 16:35:06 +0100 Date: Wed, 18 Nov 1998 16:35:06 +0100 (NFT) From: Steven Creve To: Computational Chemistry List Subject: CCL:DFT: non-local Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Maybe I should reformulate my original question: is the following correct: non-local means that the xc potential in point r depends not only on the density in r (and also gradients of rho in r, ...) but also on the density in other points r'. steven -------------------------------------------------------------------------- Steven Creve steven.creve@chem.kuleuven.ac.be Labo Quantumchemie Celestijnenlaan 200F 3001-HEVERLEE tel: (32) (16) 32 73 93 BELGIUM fax: (32) (16) 32 79 92 From chemistry-request@www.ccl.net Wed Nov 18 12:11:55 1998 Received: from smaug.wrq.com (smaug.wrq.com [150.215.17.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id MAA23759 Wed, 18 Nov 1998 12:11:55 -0500 (EST) Received: from ursula.wrq.com (root@ursula.wrq.com [150.215.11.58]) by smaug.wrq.com (8.8.6 (PHNE_14041)/8.8.6) with ESMTP id JAA22913 for ; Wed, 18 Nov 1998 09:11:55 -0800 (PST) Received: from biggeek ([150.215.151.125] (may be forged)) by ursula.wrq.com with SMTP (8.8.6 (PHNE_14041)/8.7.3) id JAA00199 for ; Wed, 18 Nov 1998 09:11:54 -0800 (PST) Received: by biggeek with Microsoft Mail id <01BE12D3.7C39E140@biggeek>; Wed, 18 Nov 1998 09:11:54 -0800 Message-ID: <01BE12D3.7C39E140@biggeek> From: Mark Alan Thompson To: "'chemistry@www.ccl.net'" Subject: ArgusLab 1.0 release on a new website Date: Wed, 18 Nov 1998 09:11:53 -0800 MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit ArgusLab 1.0 is now released. It is no longer a time-limited license, but will run without license checks indefinitely. The beta release cycle went very well. I received lots of great feedback. There are currently > 500 users. Please feel free to tell your friends and colleagues to download the program and use it. Here is the new website: http://www.seanet.com/~mthompson/ArgusLab/index.htm If you have any questions, problems, or other concerns, please send email to: mthompson@seanet.com Thanks for your help and interest Mark Thompson From chemistry-request@www.ccl.net Wed Nov 18 13:34:06 1998 Received: from ns01.sbphrd.com (firewall-user@ns01.sbphrd.com [208.198.64.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id NAA24355 Wed, 18 Nov 1998 13:34:05 -0500 (EST) Received: by ns01.sbphrd.com; id NAA28003; Wed, 18 Nov 1998 13:32:17 -0500 Received: from phinet.sbphrd.com(139.136.64.5) by ns01.sbphrd.com via smap (3.2) id xma027724; Wed, 18 Nov 98 13:31:50 -0500 Received: from phufs2.um.us.sbphrd.com by phinet.sbphrd.com; (/) id AA27343; Wed, 18 Nov 1998 13:31:50 -0500 Received: from phu198.um.us.sbphrd.com (phu198.um.us.sbphrd.com [139.136.98.47]) by phufs2.um.us.sbphrd.com (8.8.8/8.8.8/sbphrd/mh/19971204) with ESMTP id NAA25663 for ; Wed, 18 Nov 1998 13:31:48 -0500 (EST) From: M Dominic Ryan Received: (from ryanmd@localhost) by phu198.um.us.sbphrd.com (8.8.8/8.8.8) id NAA20961 for chemistry@www.ccl.net; Wed, 18 Nov 1998 13:32:59 -0500 (EST) Date: Wed, 18 Nov 1998 13:32:59 -0500 (EST) Message-Id: <199811181832.NAA20961@phu198.um.us.sbphrd.com> To: chemistry@www.ccl.net Subject: Spring ACS meeting, last call. Today is the deadline for submitting a paper to the Computers in Chemistry division of the ACS for the 1999 spring meeting in Anaheim. I will still consider submission of posters or papers to the general section for a little longer. Last minute requests for other symposia should go to the symposia chairs. If interested, please download the abstract template from the ACS web site (www.acs.org), complete it and email it to me as an attachment. You may find you cannot save it as a .doc, in which case .dot is fine. Please do not use a Mac-based attachment protocol such as binhex as I cannot decode that, but attaching via Netscape should work. If you cannot send electronically fax a copy immediately and follow up soon with surface mail. Note that I have a new fax number. Tel: 610-270-6529 Fax: 610-270-4451 email: ryanmd@mh.us.sbphrd.com Address: M. Dominic Ryan, UW2412 SmithKline Beecham 709 Swedeland Rd. King of Prussia, PA 19406 USA Program Chair Division of Computers in Chemistry American Chemical Society __ M. Dominic Ryan (610)-270-6529 SmithKline Beecham Pharmaceuticals Internet: ryanmd@mms.sbphrd.com King of Prussia, PA From chemistry-request@www.ccl.net Wed Nov 18 14:51:21 1998 Received: from mail.wesleyan.edu (mail.wesleyan.edu [129.133.1.51]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id OAA28562 Wed, 18 Nov 1998 14:51:19 -0500 (EST) Received: from localhost (yliu@localhost) by mail.wesleyan.edu (8.8.6/8.7.3) with SMTP id OAA23957; Wed, 18 Nov 1998 14:51:14 -0500 (EST) Date: Wed, 18 Nov 1998 14:51:14 -0500 (EST) From: Yongxing Liu To: chemistry@www.ccl.net cc: wwang@mail.wesleyan.edu Subject: Charmm DCD file format Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear sir, I am helping to debug a program which can convert amber trj file to Charmm DCD format and further used by Xplor. I have no experience with Charmm and Xplor though we have both packages installed. Basically I have two questions: (1) Would some one please tell me where I can find the DCD header format description without digging into the code?(e.g what's the meaning of the first 20 header varibles and their domain?) (2) Can Xplor read in charmm DCD without any modifications? Thanks a lot in advance. Yongxing Liu Department of Chemistry Wesleyan University Middletown CT 06459 Tel: 860-685-2777 From chemistry-request@www.ccl.net Wed Nov 18 15:36:27 1998 Received: from oxmail.ox.ac.uk (oxmail3.ox.ac.uk [163.1.2.9]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id PAA29171 Wed, 18 Nov 1998 15:36:26 -0500 (EST) Received: from ermine.ox.ac.uk ([163.1.2.13]) by oxmail.ox.ac.uk with esmtp (Exim 2.02 #1) id 0zgEKw-0002Ns-00 for CHEMISTRY@www.ccl.net; Wed, 18 Nov 1998 20:36:26 +0000 Received: from oums0054 (helo=localhost) by ermine.ox.ac.uk with local-smtp (Exim 2.05 #3) id 0zgEKw-0003jR-00 for CHEMISTRY@www.ccl.net; Wed, 18 Nov 1998 20:36:26 +0000 Date: Wed, 18 Nov 1998 20:36:26 +0000 (GMT) From: "Ivan I. Oleinik" To: CHEMISTRY@www.ccl.net Subject: Biosym arc file format Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear All, I am trying to write arc file in Biosym format from series of .car files. According to MSI documentation the arc file is just a set of the .car "frames" but it does not work if you just append this series in one file. It is also mentioned that the arc file is written as one record, but formatting the series as one record also does not help. Does somebody know exact format of arc files? Ivan Oleinik. ------------------------------------------------------------------------ Dr. Ivan I. Oleinik E-mail : ivan.oleinik@materials.ox.ac.uk Department of Materials University of Oxford Parks Road Oxford OX1 3PH Tel : +44 (0)1865 283325 United Kingdom Fax : +44 (0)1865 273764 ------------------------------------------------------------------------ From chemistry-request@www.ccl.net Wed Nov 18 16:14:18 1998 Received: from bioreason8 (dialup8.trail.com [209.194.109.33]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id QAA29501 Wed, 18 Nov 1998 16:14:14 -0500 (EST) Received: from bioreason.com (localhost [127.0.0.1]) by bioreason8 (950413.SGI.8.6.12/950213.SGI.AUTOCF) via ESMTP id LAA12582; Wed, 18 Nov 1998 11:31:47 -0800 Sender: dalke@bioreason.com Message-ID: <365320A3.46E235A9@bioreason.com> Date: Wed, 18 Nov 1998 11:31:47 -0800 From: Andrew Dalke Organization: Bioreason, Inc. X-Mailer: Mozilla 4.05 [en] (X11; U; IRIX 6.2 IP22) MIME-Version: 1.0 To: Yongxing Liu CC: chemistry@www.ccl.net, wwang@mail.wesleyan.edu Subject: Re: CCL:Charmm DCD file format References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Yongxing Liu asked: > I am helping to debug a program which can convert amber trj file to > Charmm DCD format and further used by Xplor. You might want to look at VMD . It contains C code to read/write binary DCD files on SGIs and HPs (the format is machine dependent). The Amber group distributes a free library for reading/writing parm files and the VMD distribution includes the library in its distribution. The end result is you should be able to use VMD to read the Amber file then write the results to a DCD file. Or you can strip the code out of VMD and roll your own solution. A couple of other package (most notably MMTK) have taken that route. > (2) Can Xplor read in charmm DCD without any modifications? I don't recall there being any problems. XPLOR ignores one of the fields that CHARMm defines. If there is a problem, you can use the same DCD library routines from UIUC to touch up the appropriate element. Andrew Dalke dalke@bioreason.com