From Bernd.Hartke@RUS.Uni-Stuttgart.DE Mon Feb 13 09:39:28 1995 Received: from dfunms.rus.uni-stuttgart.de for Bernd.Hartke@RUS.Uni-Stuttgart.DE by www.ccl.net (8.6.9/930601.1506) id IAA24554; Mon, 13 Feb 1995 08:47:56 -0500 From: Received: from servus02.rus.uni-stuttgart.de by dfunms.rus.uni-stuttgart.de with SMTP id AA15240 (5.65c8/DFUE-M1.0 for ); Mon, 13 Feb 1995 14:29:25 +0100 Received: from servus07.rus.uni-stuttgart.de by servus02.rus.uni-stuttgart.de (AIX 3.2/UCB 5.64/SERVus-1.2) id AA34408; Mon, 13 Feb 1995 14:29:24 +0100 Received: by servus07.rus.uni-stuttgart.de (AIX 3.2/UCB 5.64/4.03) id AA32662; Mon, 13 Feb 1995 14:29:23 +0100 Message-Id: <9502131329.AA32662@servus07.rus.uni-stuttgart.de> Subject: CCL: summary: distance geometry programs To: CHEMISTRY@ccl.net Date: Mon, 13 Feb 1995 14:29:22 +0100 (MEZ) Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 4622 Dear netters, last week I inquired about distance geometry programs, and I received several replies. I have attached them below in a slightly shortened form. Some of the respondents informed me that the QCPE abstract for the program #590 "DGEOM" is out of date, with respect to the form in which it is shipped. I asked QCPE about this, and they told me that the new 1995 version of DGEOM will soon be available (advance orders are being accepted already), it will be completely unix, and it will be delivered in virtually any form (including ftp delivery or pickup). Thank you very much for your help! Bernd -- Dr. Bernd Hartke e-mail: bernd.hartke@rus.uni-stuttgart.de Dep. of Theoretical Chemistry e-mail: bxh@wiffin.chem.ucla.edu University of Stuttgart Pfaffenwaldring 55 Phone: +49-711-685-4409 70569 Stuttgart FAX: +49-711-685-4442 GERMANY ================ list of replies: --------------------------------------------------------------------- From: thep@risc1.lrm.fi.cnr.it (Pornthep Sompornpisut) The program DIANA (Distance Geometry Algorithm for NMR Applications) operates in torsion angle space, performing a least-squares minimization of variable target function through manipulation of single, rotatable bonds in a generated sequence of amino acids. Diatance and dihedral angle constraints are used to calculate protein structures. The program is written in standard FORTRAN-77 and also available for Unix. However I think it's a commercial program. For further information, you can cantact Peter Guntert guentert@molbio.ethz.ch Hope this help Pornthep --------------------------------------------------------------------- From: rull@rhino.chem.ruu.nl (Ton Rullmann) I suspect that the DG program package developed by dr. Ruud Scheek from the University of Groningen might be useful. We have been using it extensively in the past. It is in Fortran, has separate modules for setup, embedding, smoothbounding etc, and the modules interact via bounds and distance matrices written to disk. I don't know anything about the current state of the program, but you might contact the author: Dr. Ruud M. Scheek Department of Biophysical Chemistry University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands Phone: +31 50 634328 Fax: +31 50 634800 Email: scheek@chem.rug.nl Good luck! Ton Rullmann. --------------------------------------------------------------------- From: wells@athens.dental.upenn.edu (Gregg B. Wells) Bernd, the description of DGEOM fromthe QCPE is out of date. The program is available in several other formats besides BACKUP. You can ask the QCPE about the availability of DGEOM for whatever platfor you want to use. Gregg Wells --------------------------------------------------------------------- From: xiao@bohr.mssm.edu (Dr. Leon Xiao) There are several places you may get the DG program for your purpose. 1. QCPE590 in Fortran, which you have already had. 2. DG-II, a commercial package comes with InsightII/NMR module by Biosym, can read in just distance constraint matrix. 3. From Prof. Tom Hayden, University of Kentucky, USA. His program may best serve your purpose. It is in C and I was helping him to develop it. I think you can get it free. You can send E-mail to hayden@ms.uky.edu or write to Prof. Tom Hayden University of Kentucky Mathematical Sciences 715 Patterson Office Tower Lexington, Kentucky 40506-0027 Good luck ! Leon Y. Xiao --------------------------------------------------------------------- From: WallyR@netcom.netcom.com (Walter E. Reiher III) The copy I bought from QCPE last fall came on a 1/4 in cartridge tape in UNIX tar format. Also, it's in FORTRAN. QCPE will deliver to you via FTP, if you prefer. I don't understand your complaint about PDB format--it's simply a common way of expressing a molecule's connection table and 3D coordinates. If anything, I find DGEOM much less protein-specific than many other programs out there. Wally --------------------------------------------------------------------- From: dixons%phvax.dnet@sb.com The DGEOM program is not all that tied to chemistry. PDB format is easy to generate or it is possible to input a bounds matrix directly and also get back out a bounds matrix if you wish. The program runs fine on Unix boxes and I am sure that you can get it in other than VAX backup format if you wish. You will need to license it from QCPE first and then if they cannot supply it in a suitable format, let me know and I will help out. Regards, Scott Dixon