Re: about internal coordinate IC statement of CHARMM force field

From: Brian Bennion (
Date: Tue Nov 25 2003 - 13:09:41 CST


First off, you don't really need to create all the IC information if you
already have a set of coordinates that describe your system. The IC
information is there only to allow psfgen and/or CHARMM to guess positions
for the atoms when few coordinates are present. If you only have a few
starting coordinates then you will have to code in all the ICs. If you
have no coordinates psfgen will not help, it needs at least 3 sets of

Second, it is the parameter file that needs the correct angles and bonds
for minimization and dynamics. This is where the time coding in angles
and such needs to be spent.


 On Tue, 25 Nov 2003,

> Dear sir,
> I need generate the topology file of CHARMM force field by myself for new
> molecule. I have two questions:
> (1)In the IC statement of CHARMM topology, many bond length,angle and dihedral
> angle are defined. When I generate them by myself, Need I list all possible bond
> length,angle and dihedral angle of that new moledcule? Or Need I only list the
> least information which can decide the configuration of this molecule?
> (2)there are some improper IC statement in the internal coordinate IC statements.
> Could you please tell me which atom need being listed as improper IC statement?
> Thank you!

**Brian Bennion, Ph.D.                                         **
**Computational and Systems Biology Division                   **
**Biology and Biotechnology Research Program                   **
**Lawrence Livermore National Laboratory                       **
**P.O. Box 808, L-448                     **
**7000 East Avenue       phone: (925) 422-5722                 **
**Livermore, CA  94550   fax:   (925) 424-6605                 **

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