Subject: RE: Software for generating conformations

From: "Warren L. DeLano" <warren..at..delanoscientific.com>
Date: Sun, 21 Sep 2003 20:52:15 -0700

Tal,

	PyMOL can do this kind of thing so long as you can uniquely
specify the atoms which make up each torsion you wish to set...

Usage: set_dihedral atom1, atom2, atom3, atom4, angle

Example: set_dihedral 11/ca, 11/cb, 11/cg, 11/cd1, 180

You could use a short Python loop to automatically adjust the torsion(s)
and then save the modified pdb files.  For example, the following
snippet:

> from pymol import cmd
for angle in (30, 65, 115, 40, 150): \
   cmd.set_dihedral("11/ca","11/cb","11/cg","11/cd1",angle) \
   cmd.save("mol_%d.pdb"%angle)

generates a set of 5 PDB files which you can then plug into some
external force-field minimizer.

Cheers,
Warren

--
mailto:warren..at..delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020

> -----Original Message-----
> From: Computational Chemistry List [mailto:chemistry-request..at..ccl.net]
On
> Behalf Of Tal Lavy
> Sent: Sunday, September 21, 2003 6:33 AM
> To: CHEMISTRY..at..ccl.net
> Subject: CCL:Software for generating conformations
> 
> 
> 
> 
> Dear All,
> 
> 
> I am looking for a free program that could generate (and output)
> conformations of molecules, according to specifications of rotations
> around
> bonds, by the user.
> 
> This means the user constructs the molecule and the program reads it
in
> PDB
> format, then the user inputs a set of angles (30, 65, 115, 40, 150
etc..)
> and
> the program outputs the transformed coordinates for the structure.
These
> structures should then undergo a force field evaluation.
> 
> Thank you very much,
> 
> Tal
> 
> 
> ===========================================================
> Tal Lavy,
> Molecular Modeling and Drug Design
> Department of Medicinal Chemistry and Natural Products
> School of Pharmacy
> Hebrew University of Jerusalem
> ISRAEL
> Phone: 972-2-6757026
> Fax: 972-2-6758925
> e-mail: tallavy..at..md.huji.ac.il
> 
> http://www.md.huji.ac.il/models
> ============================================================
> 
> 
> 
> 
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