Dear Jason
Thank you very much.
Regards
Abdul Wadood, PhD
>Asst. Prof. Dept. of Biochemistry,
>Abdul Wali Khan University Mardan-23200,
>Mardan, Pakistan.
>Office Tel: +92 137 929132
>Mobile : +92 3462623291
>
>
On Thursday, 13 November 2014, 16:57, Jason Swails <jason.swails.gmail.com> wrote:
On Thu, 2014-11-13 at 16:30 +0000, Abdul wadood wrote:
> Hi
> I am relatively new to mmpbsa calculation and trying to run mmpbsa
> calculation for protein-ligand complex interaction. I have md
> trajectory for complex system. I use the following input file
>
> Input file for running PB and GB
> &general
> endframe=50, keep_files=2,
> /
> &gb
> igb=2, saltcon=0.100,
> /
> &pb
> istrng=0.100,
> /
>
> and used the following command: MMPBSA_py -O -i mmpbsa.in -o
> Final-results.dat -sp complex-solvated.top -cp complex-nowater.top -rp
> receptor.top -lp ligand.top -y prod.mdcrd
>
> The calculation successfully completed but when I open the file
> final-results.dat I found that VDWAALS and EEL for protein and
> complex are nan.
Sounds like there is a mismatch between your trajectory files and your
coordinate files.
Try visualizing the trajectories that are generated by MMPBSA.py
(_MMPBSA_complex.mdcrd.0, _MMPBSA_receptor.mdcrd.0, ...etc.) with the
corresponding trajectory files in a molecular visualization program
(like VMD or Chimera). If the structure looks horribly warped, you know
there is a mismatch. Otherwise, you should look for another root cause.
Common problems here are that people include ions in either their
complex, receptor, and/or ligand topology files. Unless the ions are
structurally important and not part of the solvent environment, you
should not do this. If they _are_ structurally important, you need to
adjust the "strip_mask" variable to make sure MMPBSA.py does not strip
out those ions when creating the intermediate trajectory files.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Nov 14 2014 - 09:00:02 PST
