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

From: Mamon Hatmal (
Date: Thu Aug 29 2013 - 11:28:27 CDT


the steps that I use to run NAMD for a protein with a ligand

1- Create a topology file for the ligand (using either CGEN FF or swissparam) and I call it " ligand.inp"
2- Modifying the produced topology file (ligand.inp) by editing atom types manually to be compatible with NAMD
3- Using the topology file of the ligand (ligand.inp) and the standard topology file of
the proteins (top_all27_prot_lipid_na.inp) to create PSF file for the protein+ligand using VMD.
4- Run NAMD simulation (minimization+heating+MD)

My problem locates in step # 2. Editing atom types of the ligand manually is so tedious, and there are no standard topology files compatible with NAMD for such ligands ( The ligand I'm trying now is the one in 4GH2.pdb). I have no idea how to create a right topology file to use with NAMD for such ligand.


----- Original Message -----
From: Kenno Vanommeslaeghe <>
Date: Thursday, August 29, 2013 7:16 am
Subject: Re: namd-l: problem in determining atom types and charges for ligand atoms to type in the topology file
To: "" <>

> 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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