On Tue, 2014-02-25 at 13:52 -0300, George Tzotzos wrote:
> Hi everybody,
>
> I checked the archive to see if I could identify the source of error occurring “on rank 0”. I didn’t find anything that really makes sense to me. The prmtop file identified in the log (see below) loads correctly in VMD and Chimera.
>
> Any help would be much appreciated.
>
> Last but not least all patches have been applied successfully.
>
> Log file output follows below
>
> Thanks in advance
>
> George
>
>
> Loading and checking parameter files for compatibility...
> mmpbsa_py_energy found! Using /Users/3i521409/Programs/amber12/bin/mmpbsa_py_energy
> cpptraj found! Using /Users/3i521409/Programs/amber12/bin/cpptraj
> Preparing trajectories for simulation...
> 1000 frames were processed by cpptraj for use in calculation.
>
> Running calculations on normal system...
>
> Beginning GB calculations with /Users/3i521409/Programs/amber12/bin/mmpbsa_py_energy
> calculating complex contribution...
> CalcError: /Users/3i521409/Programs/amber12/bin/cpptraj failed with prmtop 4fqt_OVT.prmtop!
It seems like something went wrong with the LCPO calculation. Try
setting molsurf=1 in the &gb section of your input file. Alternatively
if the problem was with molsurf try using LCPO instead. (The surface
area calculation is run with cpptraj as of AmberTools 13).
In the meantime, can you send me the 4fqt_OVT.prmtop file and a
structure for it? (A restart, PDB, or trajectory with 1 frame works).
Thanks!
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Feb 25 2014 - 12:30:09 PST
