On Tue, Dec 1, 2015 at 1:59 PM, Atila Petrosian <atila.petrosian.gmail.com>
wrote:
> Dear Jason,
>
> Very thanks for your answers.
>
> I have 9 protein-ligand complexes.
>
> The errors in my previous email were related to number 1 complex.
>
> I did GB and quasi-harmonic calculations for number 2 complex and
> I encountered with following error:
>
> Running calculations on normal system...
>
> Beginning GB calculations with
> /share/apps/amber/amber14/bin/mmpbsa_py_energy
> calculating complex contribution...
> calculating receptor contribution...
> calculating ligand contribution...
>
> Beginning quasi-harmonic calculations with
> /share/apps/amber/amber14/bin/cpptraj
> Error: # atoms in TRX file (0) does not match # atoms in parm comp.prmtop
> (5042)
> Error: Could not set up _MMPBSA_avgcomplex.pdb for reading.
> Error: reference: Could not set up trajectory.
>
This is weird. What's happening is that cpptraj is trying to read this
PDB file as a TRX file (which I believe is a GROMACS-format trajectory).
This obviously won't work. What does _MMPBSA_avgcomplex.pdb look like?
Can you create a compressed tarball with _MMPBSA_avgcomplex.pdb and
comp.prmtop and email it to me off-line so I can look at it?
1 errors encountered reading input.
> File "/share/apps/amber/amber14/bin/MMPBSA.py.MPI", line 96, in <module>
> app.run_mmpbsa()
> File "/share/apps/amber/amber14/bin/MMPBSA_mods/main.py", line 218, in
> run_mmpbsa
> self.calc_list.run(rank, self.stdout)
> File "/share/apps/amber/amber14/bin/MMPBSA_mods/calculation.py", line 79,
> in run
> calc.run(rank, stdout=stdout, stderr=stderr)
> File "/share/apps/amber/amber14/bin/MMPBSA_mods/calculation.py", line
> 363, in run
> Calculation.run(self, rank, stdout=self.output)
> File "/share/apps/amber/amber14/bin/MMPBSA_mods/calculation.py", line
> 148, in run
> self.prmtop))
> CalcError: /share/apps/amber/amber14/bin/cpptraj failed with prmtop
> comp.prmtop!
> Error occured on rank 1.
> Exiting. All files have been retained.
>
>
> I used following command line:
>
> mpirun -np 8 $AMBERHOME/bin/MMPBSA.py.MPI -O -i mmgbsa_qh.in -o
> mmgbsa_qh.dat -sp
> comp_sol.prmtop -cp comp.prmtop -rp pr.prmtop -lp lig_h.prmtop -y
> autoimaged.binpos &
> I did GB calculation without any problem. I want to obtain entropy
> proportion.
>
> What is your suggestion?
>
Try a calculation with JUST the quasi-harmonic entropy part, and do that
in serial (that calculation is not parallelizable so using multiple
processors won't help anway). See if that works.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Dec 01 2015 - 11:30:04 PST
