[AMBER] Input file (_MMPBSA_gb.mdin) doesn't exist

From: Mu Xia <muxiachuixue.163.com>
Date: Sat, 9 Nov 2013 10:19:35 +0800 (CST)

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
   verbose=1, interval=5,
  igb=5, saltcon=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
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