problem in determining atom types and charges for ligand atoms to type in the topology file

From: Mamon Hatmal (
Date: Thu Aug 29 2013 - 06:03:17 CDT

Hi NAMD users,

For creating PSF file for a ligand in a protein using VMD, we have to use an input file (topology file) for the ligand (in addition to the topology file of the protein) which contains atom types. My problem is how to determine atom types of that ligand in the topology file, I tried to do it manually but it is tedious and prone to many errors.


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