Re: [AMBER] mmgbsa_CalcError

From: Atila Petrosian <>
Date: Tue, 1 Dec 2015 22:29:15 +0330

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
  calculating complex contribution...
  calculating receptor contribution...
  calculating ligand contribution...

Beginning quasi-harmonic calculations with
Error: # atoms in TRX file (0) does not match # atoms in parm comp.prmtop
Error: Could not set up _MMPBSA_avgcomplex.pdb for reading.
Error: reference: Could not set up trajectory.
        1 errors encountered reading input.
  File "/share/apps/amber/amber14/bin/", line 96, in <module>
  File "/share/apps/amber/amber14/bin/MMPBSA_mods/", line 218, in
run_mmpbsa, self.stdout)
  File "/share/apps/amber/amber14/bin/MMPBSA_mods/", line 79,
in run, stdout=stdout, stderr=stderr)
  File "/share/apps/amber/amber14/bin/MMPBSA_mods/", line
363, in run, rank, stdout=self.output)
  File "/share/apps/amber/amber14/bin/MMPBSA_mods/", line
148, in run
CalcError: /share/apps/amber/amber14/bin/cpptraj failed with prmtop
Error occured on rank 1.
Exiting. All files have been retained.

I used following command line:

mpirun -np 8 $AMBERHOME/bin/ -O -i -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

What is your suggestion?
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Received on Tue Dec 01 2015 - 11:30:03 PST
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