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

From: Mamon Hatmal (
Date: Sun Sep 01 2013 - 16:16:38 CDT

Thanks Kenno for your patience and for the great help. I started to make short simulations.


----- Original Message -----
From: Kenno Vanommeslaeghe <>
Date: Thursday, August 29, 2013 2:20 pm
Subject: Re: namd-l: problem in determining atom types and charges for ligand atoms to type in the topology file
To: "" <>

> 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):
> top_all36_cgenff.rtf
> par_all36_cgenff.prm
> 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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