You appear to be selecting 2 residues in VMD -- you are calculating the
pairwise interaction between residues 917/919 and residue 918. Amber does
not do this. The value you're getting from NAMD (I presume!), is a
double-sum over all atoms i, j where i is in residue 917 or 919 and j is in
residue 918. Amber will do the pairwise interaction between individual
residues only, so I would expect the NAMD results to match the Amber
results if you added the pairwise 917-918 and 919-918 energies together.
I think this is where your factor of 2 is coming from -- you have roughly
twice as many interactions being counted.
HTH,
Jason
On Thu, Jan 31, 2013 at 1:10 AM, dbaogen <dbaogen.gmail.com> wrote:
> Dear all,
>
> I want to calculate the pairwise interaction energy (VDW and
> Electrostatic) of two residues. In AMBER 11 software, MMPBSA.py script is
> used by using "idecomp=4" option in the input file. And In VMD 1.9.1
> software, NAMDenergy plugin is used, and the force field parameter is also
> amber type. The detail information of parameter settings is as follow. But
> for the calculated results, the value of interaction energy (VDW and
> Electrostatic ) of NAMDEnergy is two fold of the counterpart of MMPBSA.py.
> I don't know whether there is difference of scaling factor between these
> two methods in calculating VDW and electrostatic energy. Would you like to
> give me some help? Thanks !
>
>
> Best wishes
>
> Yours Sincerely
>
> Duan Baogen
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> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Jan 31 2013 - 04:30:03 PST
