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

From: Branko (
Date: Thu Aug 29 2013 - 12:08:30 CDT


VegaZZ ( include InpMerge utility. Try with this


On 8/29/2013 6:28 PM, Mamon Hatmal wrote:
> Hi,
> 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.
> Best,
> ----- 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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