Subject: summary: conformer generator

From: "Ivar Martin" <[email-masked]>
Date: Mon, 13 Feb 95 18:33:34 EST

Dear CCL people,

I asked you about programs which would generate a large variety of 
conformations as input for MOPAC 6.0 which I currently use.
Several people asked me to share the answers with them, so I give you
a summary.

In addition to current responses I found from CCL archieves:
        - MOLGEN for PC
        - PowerSearch for MS-Windows from Tripos
very many good words about   - MacroModel
        - DGEOM from QCPE

I would like to thank everyone who responded, namely

 Peter Burk
 Bill Ross
 E. Lewars
 Brian T. Luke
 Karl F.Moschner
 Jerzy Rudzinski
 Chris L. Waller
 Mike Tennant
 Andy Holder

====================================================================
My original question was:

please suggest me a program which takes up the given geometry
(cartesian or internal) and generates a lot of conformers from that 
for the MOPAC input. It would be nice if the program works in UNIX.
(FORTRAN source would be excellent).

Thank you!
_______________________________
Dr. Ivar Martin
Department of Bioorganic Chemistry           tel: +372 2 526510
Institute of Chemistry                       fax: +372 2 536371
Akadeemia tee 15 EE0026                   e-mail: [email-masked]
Tallinn, ESTONIA
=====================================================================

ANSWERS in chronological order:
-------------------------------------------------------
From: Peter Burk <[email-masked]>
[my free translation into english... I.Martin]

Dear Ivar,

I have the perl's script which does the job you need. Only
it is not very smart - it doesn't check the identical
geometries and interatomic distances. 

-- 
Peeter Burk, Ph.D.                      Jakobi 2, EE2400 Tartu, Estonia
Institute of Chemical Physics           Phone (372-7) 441-453           
Tartu University                        Fax   (372-7) 441-453           
Estonia                                 E-mail [email-masked]

-------------------------------------------------------------------
From: [email-masked] (Bill Ross )

A recent CCL post mentioned using Amber for generating
a spectrum of conformations using high-temperature molecular
dynamics; in case you are interested in this option, here
is the Amber info.

There is a mail reflector for Amber users and people interested in
Amber. A major part of the traffic is the bugfix announcements.
 [email-masked]              [email-masked]
and mail to either
 [email-masked]      [email-masked]
for administrative requests.

Bill Ross

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From: "E. Lewars" <[email-masked]>

The PC program pcGlobal generates a set or conformers 
randomly (stochastically).
The program is sold by Serena Software, Box 3076, Bloomington,IN 47402-3076.
Email: [email-masked]   Kevin Gilbert, President.

The program Spartan will search through the possible conformers and calc
their energies; Spartan is UNIX-based and has MM, ab in., and semiemp.
Contact Wavefunction, Inc, 18401 von Karman, Suite 210, Irvine, CA 92715
USA.  Email [email-masked]  or  [email-masked]

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

Dr. Martin,

When I ported MOPAC7 from a Sun to the IBM RS/6000, I modified it
so that it will generate multiple initial conformations of a molecule
>from a single input file (see Journal of Computational Chemistry, 15
(1994) 1176-1185).  If this will fit your needs, you can order the
program from the Quantum Chemistry Program Exchange (QCPE).

Brian T. Luke, Ph.D.

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

I have used the conformational search routines in the commercial package 
Sybyl to generate conformers and then submit the individual structures for 
single point calculations using MOPAC V6.0.  You could also use any other 
3rd party package for which they provide an interface or create your own 
using macros.  Unfortunately, they're unlikely to provide the source code.

 _______________________________________________________________________
/                                                                       \ 
| Comments are those of the author and not Unilever Research U. S.      |
|                                                                       |
| Karl F. Moschner, Ph. D.                                              | 
|                                                                       | 
| Unilever Research U. S.      e-mail: [email-masked] | 
| 45 River Road                Phone:  (201) 943-7100 x2629             | 
| Edgewater, NJ 07020          FAX:    (201) 943-5653                   | 
\_______________________________________________________________________/

------------------------------------------------------------------------
From: Jerzy Rudzinski  <[email-masked]>

Dear Dr Martin,
Thare are commercial packages that do the job. For sure I know two
that is ANCHOR II from Fujitsu Limited (good for SUN and some
other UNIX machines) and Spartan.  I am sure other commercial programs
can also do.
If you get responces, please share the info. I am also interested in
good conformational generators.

Wishes, Jerzy Rudzinski

-----------------------------------------------------------------------
From: "Dr. Chris L. Waller" <[email-masked]>

I have an SPL (Sybyl Programming Language) script which does exactly
what you desire. The only catch is - you must have Sybyl to run it.

If you can use it, I will gladly send a copy.

********************************************************************
*Chris L. Waller, Ph.D.                          PHONE 919-541-7976*
*Research Chemist                                FAX   919-541-5394*
[email-masked]                                          *
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*endorsement by the United States Environmental Protection Agency. *
********************************************************************

----------------------------------------------------------------------
From: Mike Tennant <[email-masked]>

Ivar,
 you can use macromodel to generate a set of unique conformations 
and then extract these confs to individual mopac input files using babel. 
Both progs run under unix.

  Mike

---------------------------------------------------------------------
From: Andy Holder <[email-masked]>

Dear Dr. Martin,

  The simulated annealing subroutine in our AMPAC 5.0 with Graphical
User Interface is designed to help with this problem rather directly.
The algorithm generates candidate conformers and optimizes them in AMPAC 
using our advanced convergence algorithms.  The method keeps up with 
previous located structures and discards duplicates.  It also has a 
number of nice penalty features that eliminate poor candidates early on.  
The methodology is "annealing" only in the conformer generation step.
The sorting and grouping step is very intelligent and is built around
some literature heuristic algorithm methods.  The GUI also collects and 
organizes the results in a nice graphics window.
  We are currently running a demonstration promotion, so if anyone would 
like to try it out, get in touch with me as noted below.

  Andy Holder

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      DR. ANDREW HOLDER
     President, Semichem

Semichem, Inc.            ||  Internet Addr: [email-masked]
7128 Summit               ||  Phone Number:  (913) 268-3271
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