Hi all,
My system is a normal protein-ligand complex. I recently tried to conduct the binding free energy calculation after the MD simulation using Amber12+AmberTools13. The following is the input file:
Input file for running PB and GB
&general
verbose=1, interval=5,
strip_mask=":WAT:Cl-",
/
&gb
igb=5, saltcon=0.100
/
&pb
istrng=0.100,
/
And the command line:
mpirun -np 8 MMPBSA.py.MPI -O -i mmpbsa.in -o MMPBSA_BIND_3CH6_M1.dat -sp 3CH6_M1_wat.prmtop -cp 3CH6_M1.prmtop -rp 3CH6.prmtop -lp M1.prmtop -y ../md/production27.mdcrd.gz ../md/production28.mdcrd.gz ../md/production29.mdcrd.gz ../md/production30.mdcrd.gz > progress.log 2>&1
After 1-2 minutes, the job terminated with the following error:
Beginning GB calculations with /home/Amber/AM12/amber12/bin/mmpbsa_py_energy
calculating complex contribution...
IOError: Input file (_MMPBSA_gb.mdin) doesn't exist
I have tried to add -make-mdin into the command line or use keep_files=2 in the input file, but no solution. However, when I changed back to Amer12+AmberTools12 or Amber11+AmberTools1.5, everything is OK.
BTW, my system is RHEL 5.4_x64, and the compiler is GNU.
My question is: how to get rid of the problem? Is there something wrong with my installation?
Many thanks!
Mu Xia,
Zhejiang University, China
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Received on Fri Nov 08 2013 - 18:30:02 PST
