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

From: Kenno Vanommeslaeghe (
Date: Thu Aug 29 2013 - 09:00:58 CDT

I believe you mentioned in an earlier post you're using the CGenFF program
at , which never introduces new atom types - it just uses
the ones in the main files of the CGenFF force field. For the purpose of
running *NAMD*, one needs to read both the main parameter file and the
toppar stream file generated by the CGenFF program, as documented on my
website. Similarly, in *psfgen*, I *believe* it is possible to read both
the main topology file and the toppar stream file; if I'm not mistaken,
I've seen an example of this earlier on this list. As for *VMD*, I have no
idea whether it has the same capability to read multiple topology files;
perhaps the experts here can fill that in (and correct me if I'm wrong
about psfgen).

If all else fails, one can always copy-paste the MASS entries from the
main file to the toppar stream file; this should be pretty
straightforward. Note, however, that doing so doesn't eliminate the need
to stream both parameter files into *NAMD*.

On 08/29/2013 07:03 AM, Mamon Hatmal wrote:
> 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.
> Best,

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