Hello All,
I am getting this error while running gb and decomp using Amber12 SANDER.
gb ran successfully in separate. But when try to run decomp with the same
set of top files it is giving this error :
mmpbsa amber error failed with prmtop com.top!
But I checked it prepared some files like _MMPBSA_gb_decomp_com.mdin,
_MMPBSA_dummycomplex.inpcrd, _MMPBSA_complex.mdcrd.0, (the same for ligand
and receptor)_MMPBSA_normal_traj_cpptraj.out, _MMPBSA_restrt.0,
_MMPBSA_complex_gb.mdout.0
I checked the file _MMPBSA_complex_gb.mdout.0 ,it started writing and
stopped abruptly after "minimizing coord set # 60"
Here is my mmpbsa.in:
MMPBSA.py input file for running GB in serial
&general
startframe=1, endframe=12500, interval=50,
#receptor_mask=:89-180, ligand_mask=:1-88, (required for ALA scan)
entropy=0,
keep_files=1,
/
&gb
igb=5, saltcon=0.1,
/
&decomp
idecomp=2,
/
Please help.
Sucharita
Sucharita Dey,PhD, Research Fellow, Cancer Science Institute of Singapore,
National University of Singapore. 14, Medical Drive, #12-01, Singapore
117599. Tel: (65) 90355220, email: csisd.nus.edu.sg
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Received on Sun Aug 31 2014 - 23:00:02 PDT
