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 - 14:30:04 PST
