On Fri, Nov 8, 2013 at 9:19 PM, Mu Xia <muxiachuixue.163.com> wrote:
> 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?
>
Try updating your installation. Re-run configure and then recompile.
If this doesn't work, let me know.
All the best,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sat Nov 09 2013 - 07:00:02 PST
