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 - 16:05:27 CDT

On 08/29/2013 12:28 PM, Mamon Hatmal wrote:
> 1- Create a topology file for the ligand (using either CGEN FF or swissparam) and I call it " ligand.inp"

Please do not use SwissParam; its approach of combining CHARMM L-J
parameters with MMFF94 charges and dihedrals is fundamentally flawed. If
for some reason (please let us know the reason) you're not happy with
CGenFF, you can give MATCH from the Charlie Brooks lab a try. While I feel
ParamChem has a couple of advantages over MATCH (I'm obviously not a
neutral party), at least there are no _fundamental_ problems with the latter.

> 2- Modifying the produced topology file (ligand.inp) by editing atom types manually to be compatible with NAMD

You must mean VMD. As I said in my last message, the output of CGenFF is
directly compatible with NAMD. The recommended sequence of NAMD commands
on my website really works - we're using them all the time.

> 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.

Whatever the problem might be, changing the atom types is *not* the right
solution. Please:

- download the CGenFF force field:

- look at the following files (which we call the "main" files):
Note that all the atom types are defined there - no need to change anything!

- read my previous post again. In general, before asking people for help,
first make sure you're prepared to listen carefully to their answer.

> 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.

I don't think your problem is step #2 - I think you're doing something
wrong in step #3 and are incorrectly inferring from it that you need to
change the atom types. Again, I'm no expert in psf preparation with tools
other than CHARMM, but there are other people on this list who should be
able to help you.

One approach that works reasonably well and does not require CHARMM is to
use the CHARMM-GUI website; it's very friendly to inexperienced users.
You can just give it the PDB ID of your protein-ligand system of choice
and it generates xplor psf files along with ready-to-run NAMD inputs.

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