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.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Sep 14 2015 - 19:00:03 PDT
