[AMBER] mmpbsa error

From: Lara rajam <lara.4884.gmail.com>
Date: Mon, 14 Sep 2015 21:40:49 -0400

Dear Amber

I am trying to do the MMPBSA calculation , earlier I was generating the
parameters with ff99SB and I was able to run mmpbsa.py

Now I generated the prmtop using ff12SB , I was not able to run mmpbsa
calculation, the error is as below I am running in serial mode. I again
generated all the prmtop and did a try, the error is the same and my input
is below

INPUT file

Input file for running PB and GB in serial

&general

   endframe=50, keep_files=2,

/

&gb

  igb=2, saltcon=0.100,

/

&pb

  istrng=0.100,

/


OUT PUT ERROR !

[TEST.NEMO dr2]$ $AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -o
FINAL_RESULTS_MMPBSA.dat -sp solvated_di.prmtop -cp complex.prmtop -rp
protein.prmtop -lp ligand.prmtop -y *.mdcrd

Loading and checking parameter files for compatibility...

mmpbsa_py_energy found! Using
/home/TEST/AMBERHOME/amber14/bin/mmpbsa_py_energy

cpptraj found! Using /home/TEST/AMBERHOME/amber14/bin/cpptraj

Preparing trajectories for simulation...

50 frames were processed by cpptraj for use in calculation.


Running calculations on normal system...


Beginning GB calculations with
/home/TEST/AMBERHOME/amber14/bin/mmpbsa_py_energy

  calculating complex contribution...

  File "/home/TEST/AMBERHOME/amber14/bin/MMPBSA.py", line 96, in ?

    app.run_mmpbsa()

  File "/home/TEST/AMBERHOME/amber14/bin/MMPBSA_mods/main.py", line 218, in
run_mmpbsa

    self.calc_list.run(rank, self.stdout)

  File "/home/TEST/AMBERHOME/amber14/bin/MMPBSA_mods/calculation.py", line
79, in run

    calc.run(rank, stdout=stdout, stderr=stderr)

  File "/home/TEST/AMBERHOME/amber14/bin/MMPBSA_mods/calculation.py", line
147, in run

    raise CalcError('%s failed with prmtop %s!' % (self.program,

CalcError: /home/TEST/AMBERHOME/amber14/bin/mmpbsa_py_energy failed with
prmtop complex.prmtop!

Exiting. All files have been retained.
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Received on Mon Sep 14 2015 - 19:00:03 PDT
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