Subject: CCL: summary: distance geometry programs

From: <[email-masked]>
Date: Mon, 13 Feb 1995 14:29:22 +0100 (MEZ)

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program #590 "DGEOM" is out of date, with respect to the form in which it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: [email-masked]
Dep. of Theoretical Chemistry     e-mail: [email-masked]
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: [email-masked] (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
[email-masked]

Hope this help
Pornthep

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From: [email-masked] (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: [email-masked]

Good luck!
Ton Rullmann.

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From: [email-masked] (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: [email-masked] (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
     [email-masked]
   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: [email-masked] (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: [email-masked]

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