Thank you very much. Indeed the protein topology includes a water molecule. In fact, This water molecule appears to be conserved and I’m trying to investigate its effect on ligand binding.
I’m pretty sure that all bug fixes were applied. However, I shall recompile tomorrow and I’ll let you know.
Regards
George
On Feb 26, 2014, at 7:13 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Wed, Feb 26, 2014 at 3:18 PM, George Tzotzos <gtzotzos.me.com> wrote:
>
>> Apologies to burden the list with this problem.
>>
>> I've run MMPBSA.py.MPI on a different simulation. I encountered the same
>> problem. Please see attached mdout and log files.
>>
>> I wonder if I should recompile and run MMPBSA again.
>>
>> Your suggestions will be most welcome.
>>
>
> I downloaded your files and tried them out. I did get an error with
> cpptraj when I tried to compute the surface area using LCPO (which is the
> default surface area method) with an error message:
>
> Error: Atom 2016 in mask :* does not belong to solute.
>
> Warning: Setup failed for [surf thing :* out test.dat]: Skipping
>
> ----- 4fqt_OVT.inpcrd (1-1, 1) -----
>
> 100% Complete.
>
> This occurs because including solvent in a surface area calculation is
> unusual, and this is a check in cpptraj to prevent a mistake. (Your
> topology file has a WAT residue.) This issue was addressed by update.5 for
> AmberTools 13 (see http://ambermd.org/bugfixesat.html). Can you check that
> these bug fixes are applied and recompile AmberTools?
>
> If it still doesn't work, I think I'm going to need to be able to reproduce
> this error locally on one or two frames.
>
> Thanks,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Wed Feb 26 2014 - 15:00:03 PST
