Re: about charmm topology file

From: Brian Bennion (
Date: Wed Nov 05 2003 - 10:27:51 CST

Hello Zhilei,

Lets put a few things in order here. First, vmd is not a molecular editor
never has been, won't be any time soon.
Second your estradiol residue entry in your topology file should contain
the atoms in the order they appear in your pdb file for psfgen to have a
good chance of getting the coordinates correct.

Third the ICs are not the cause of the psfgen error.

Fourth, parameterizing a ligand like estradiol is not easy. (See previous
post this list from myself.) For example there are at least 158 dihedral
angles that namd needs info on, granted most of these are degenerate so
you will only need to add maybe 70 ICs. I have been working on this
ligand for 3 weeks and am almost done.

Its pitifull that other researchers that have published their MD work with
estradiol don't include the parameter lists, it makes their work very
suspect indeed....

I am a member of the biocore-era group so we can talk more there if you


 On Wed, 5 Nov 2003, Zhilei Chen wrote:

> Hi,
> I am trying to build a charmm topology file for my ligand estradiol. I
> finished type in the MASS, Charge, Bond, Double, and IMPR. I suppose vmd can
> auto generate all the angle and bond, based on the pdb file. When I use psfgen
> to generate pdb and psf, it popped out the message "Warning : failed to set
> coordinate for atom ..." and "Warning: failed to guess coordinates for 44
> atoms".
> I tried to add some IC to the topology, but there are too many. I don't know
> whether is the necessary to add the IC for every possible combination in the
> ligand to the topology file. After I painstakingly typed in 15 ICs to the
> topology file and try to run the psfgen again, it made no difference.
> I don't know what is happening.
> Can anybody help?
> zhilei

**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) 422-6605                 **

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