From haney@netcom.com Tue Jul 5 21:50:42 1994 Received: from netcom.com for haney@netcom.com by www.ccl.net (8.6.9/930601.1506) id VAA21421; Tue, 5 Jul 1994 21:31:49 -0400 Received: by netcom.com (8.6.8.1/SMI-4.1/Netcom) id SAA03453; Tue, 5 Jul 1994 18:33:11 -0700 From: haney@netcom.com (Dr. David N. Haney) Message-Id: <199407060133.SAA03453@netcom8.netcom.com> Subject: AMBER USERS To: CHEMISTRY@ccl.net Date: Tue, 5 Jul 1994 18:33:11 -0700 (PDT) X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 4534 The following is a summary of responses that I received regarding graphics programs to visualize AMBER results. ORIGINAL POST: I was wondering if anyone has developed a tool to assist in the viewing of AMBER coordinate files. In particular, it seems that someone must have dealt with the potential of converting AMBER's coordinate files mdcrd and mincor for MINMD to a file type that could be read by Sybyl, Quanta or InsightII. As far as I can tell BABEL cannot deal with this problem. Abbreviated responses: ----------------------- From: vepa@rox.mel.dbe.csiro.au (Vidana C. Epa) The ANAL module of AMBER v.4.0 can convert 'mincor' files into PDB format, while the CARNAL module (not yet a standard AMBER module) can convert 'mdcrd' files into PDB format. Once it's in PDB format, of course, it may be viewed with any mol. modelling graphical interface. From: David Case The usual procedure is to create "PDB" format files, which the programs you mention above can read. You can do this through ANAL, or with the program ambpdb. I usually use the latter, but don't remember if it is in the 4.0 distribution or not...it's certainly in 4.1, probably in src/etc. Or I can mail you a copy if you like. From: Jeff Dyason I believe that you can convert the amber trajectory files into a whole heap of pdb files (i.e. file1.pdb, file2.pdb, .... fileN.pdb), these can then be converted to at least an InsightII .arc file by a bcl macro, which I distributed via the dibug mailing list last year. The macro is not fool proof, because of the naming of some atoms, but this is fairly easily tailored to a particular system. We generally use it here to analyse x-plor structures derived from nmr data, although I think someone has used it for amber files. If you want a copy of the macro or any further information just e-mail me. From: charlie@iris5.icr.ac.uk (Charles Laughton) Here we use Terry Lybrand's program MD-Display to view our AMBER md snapshot files. It works fine for us, though it may not offer all the functionality that Sybyl, Quanta or InsightII might give you. I'm sorry, I can't find an e-mail address for Terry for you (but he's at the University of Washington, Seattle). From: ross@cgl.ucsf.edu (Bill Ross ) If those progs read pdb, carnal will do the job for mdcrd; pdbgen & carnal do it for mincor.. the other progs' user communities probably have stuff too; there is a parm file routine in carnal that can be adapted to get the bond info & atom types for writing converted files. From: david@auvergne.cbs.univ-montp1.fr (David Cregut) We modified the PDBGEN utility from AMBER 4.0 in order to read mdcrd and parm files from AMBER and to write a file to the Insight II archive format. The trajectory can then be viewed using the analysis module of Insight II. From: K Bryson A little program called 'groch' in the 'util' directory of Quanta can be used to convert mdcrd files from amber to DCD animation files for Quanta. You also need to 'Import' a pdb file from amber to Quanta to get the topology of the structure into quanta. ( Originally groch was for GROMOS mdcrd file to Quanta DCD conversion, but Amber hasn't changed the format of this output file from the original GROMOS standard. ) From: mitchell@bdrc.bd.com (Mike Mitchell) There are already Sybyl Programming Language (SPL) and C language utilies to convert AMBER trajectory data to a Sybyl .his file. Look in $TA_ROOT/spl and get the ambertosybyl.spl script. From: Pat Walters I'm the author of Babel. If you send me samples and specifications for some of these file formats I'd be glad to add them to Babel. Actually I have an AMBER 4.0 manual so if the specs are in the manual all I'll probably need are a few sample files. It usually takes me me very little time to do this. From: "Jeffrey P. Jones" AMBER files can be converted to SYBYL readable files by the macro ambertosybyl. SYBYL> take $TA_ROOT/tables/sample.macros SYBYL> ambertosybyl Answer the questions and wait a long time for a history file. -- ************** David N. Haney, Ph.D. **************** * Haney Associates Phone - 619-566-1127 * * 12010 Medoc Ln. * * San Diego, CA 92131 Fax - 619-586-1481 * ************** Email - haney@netcom.com ***************