CCL: summary: distance geometry programs

 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 program #590 "DGEOM" is out of date, with respect to the form in which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 "at@at"
 rus.uni-stuttgart.de
 Dep. of Theoretical Chemistry     e-mail: bxh "at@at" 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:
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 From: thep "at@at" 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 "at@at" molbio.ethz.ch
 Hope this help
 Pornthep
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 From: rull "at@at" 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 "at@at" chem.rug.nl
 Good luck!
 Ton Rullmann.
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 From: wells "at@at" 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
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 From: xiao "at@at" 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 "at@at" 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
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 From: WallyR "at@at" 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
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 From: dixons%phvax.dnet "at@at" 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