On Wed, Sep 18, 2013 at 3:27 AM, Sumra Wajid Abbasi 30-FBAS/MSBI/F09 <
sumra.msbi30.iiu.edu.pk> wrote:
> Dear Users
>
> I am trying to carry out binding free energies calculations for my
> protein-ligand docked complex using MMPBSA.py, AMBERTools12. All
> calculations run smooth but at the end when i checked results file i found
> that GB calculations for ligand were ok but in case of PB calculations for
> ligand following problem occurred.
>
> Ligand:
>
> G solv nan nan
> nan
>
> TOTAL nan nan
> nan
>
> Differences (Complex - Receptor - Ligand):
>
> DELTA G solv nan nan
> nan
>
> DELTA TOTAL nan nan
> nan
>
>
> Please help me to address the problem.
>
You didn't include any details that would help us debug this problem.
What term is actually NaN? EPB, ECAVITY, EDISPER? Do the GB results
appear reasonable? What happens when you visualize the MMPBSA.py-generated
trajectory files (_MMPBSA_complex.mdcrd, _MMPBSA_receptor.mdcrd, and
_MMPBSA_ligand.mdcrd) with the corresponding topology files? Do they look
sensible? (Incompatibilities between topology files and trajectories are
very easy to spot).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Sep 18 2013 - 04:30:03 PDT
