about charmm topology file

From: Zhilei Chen (zchen4_at_students.uiuc.edu)
Date: Wed Nov 05 2003 - 10:00:56 CST


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

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?


This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:37:05 CST