Dear Jason
NAN= No Atom Name
EPB/EGB = the electrostatic contribution to the solvation free energy
calculated by PB or GB respectively
ECAVITY = nonpolar contribution to the solvation free energy calculated by
an empirical model
I have visualized MMPBSA.py generated mdcrds using VMD...what i feel is
there are abnormalities in ligand geometry and also few in receptor..
Sumra Wajid Abbasi
PhD Scholar
Computational Biology Lab, National Center for Bioinformatics
Quaid-e-Azam University, Islamabad-45320 Pakistan.
On Thu, Sep 19, 2013 at 1:12 PM, Sumra Wajid Abbasi 30-FBAS/MSBI/F09 <
sumra.msbi30.iiu.edu.pk> wrote:
> Dear Jason
>
> NAN= No Atom Name
> EPB/EGB = the electrostatic contribution to the solvation free energy
> calculated by PB or GB respectively
> ECAVITY = nonpolar contribution to the solvation free energy calculated by
> an empirical model
>
> I have visualized MMPBSA.py generated mdcrds using VMD...what i feel is
> there are abnormalities in ligand and also few in receptor..
>
> Attached are the images of what i have visualized..
>
> Regards
>
>
> Sumra Wajid Abbasi
> PhD Scholar
> Computational Biology Lab, National Center for Bioinformatics
> Quaid-e-Azam University, Islamabad-45320 Pakistan.
>
>
> On Wed, Sep 18, 2013 at 4:08 PM, Jason Swails <jason.swails.gmail.com>wrote:
>
>> 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
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Thu Sep 19 2013 - 01:30:02 PDT
