Re: MMPBSA Energy Calculations using VMD (Post-Processing)

From: James Starlight (
Date: Mon Apr 14 2014 - 04:23:01 CDT

And some additional questions:

1 ) In manual I've found that for this script four topology files
should be provided besides the input file:
-sp solvated_prmtop \ -cp complex_prmtop \ -rp receptor_prmtop \ -lp
should this files be taken from the param files provided in the namd files
as you can see below or alternatively obtained from the resulted psf ?

parameters ../parameters/par_all27_prot_lipid.inp
parameters ../parameters/ligand.prm
parameters ../parameters/water_ions.prm

2) What difference in resulted dG should be expected between calculations
in (PB) or (GB) regimes assuming that I'll try to estimate free energy of
the binding hydrophobic ligands (contribution from the polar interactions
of only up to 30%) to the membrane receptors ?


2014-04-14 9:56 GMT+04:00 James Starlight <>:

> Many thanks for suggestions!
> I'll try to wait AmberTools 14 and test it with the namd's produced
> trajectory and all input files.
> One question: can I use parametrization of my system done in charm-like
> force field instead of amber (including ligand parametrized in cgenff)? As
> I noticed amber need slightly shorter cutoffs for non-bonded terms in
> comparison to charm indication difference in this terms between both force
> fields.
> Thanks for help,
> James
> 2014-04-12 15:53 GMT+04:00 Jason Swails <>:
>> On Sat, Apr 12, 2014 at 2:53 AM, James Starlight <>wrote:
>>> Dear all,
>>> I also looking for the possibility to calculate free energy of ligand
>>> binding using script and NAMD trajectory.
>>> As I know in NAMD I can make parametrization of my system using amber
>>> (not charmm) force field. So I need (i) proper way to parametrize ligand in
>>> amber (ii) convert dcd to amber-like trajectory
>> For (i) you can use antechamber from AmberTools. Your step (ii) is
>> unnecessary. understands DCD files natively.
>> Also, if you've used the CHARMM force field and created the PSF file with
>> VMD, the upcoming release of AmberTools 14 (within a week) will have a
>> version of "chamber" that can convert VMD-generated PSF files into topology
>> files can understand.
>> Hope this helps,
>> Jason
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher

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