Have you tried changing the source code?
http://archive.ambermd.org/201008/0400.html
Good luck!
-Bill
On Tue, Sep 21, 2010 at 10:57 AM, Chanchal <chanchal.kar.gmail.com> wrote:
> Dear All,
> I am using the new parallel version MMPBSA.py.MPI to calculate the
> binding free energy of a steorid+protein complex. Although my GB
> calculation
> was successful, but the PB calculation failed. I checked _MMPBSA_*_pb.mdout
> file and there I got the following error message:POST-PROCESSING OF
> TRAJECTORY ENERGIES
> trajectory generated by
> ptraj
> minimizing coord set # 1
> PB bomb in pb_reslist(): maxnbr too small
>
> Then I use the command -make-mdins to create the _MMPBSA_pb.mdin file so
> that I can edit it. Here is the job script file.
> #!/bin/bash
>
> ##############################################################
> #$ -S /bin/bash
>
> #$ -q "*"
> #$ -N w5AD
>
> #$ -m bae
> #$ -M Parimal.Kar.mpikg.mpg.de
> #$ -pe openmpi 1
>
> #$ -cwd
> #$ -o $JOB_NAME_$JOB_ID.OUT
> #$ -e $JOB_NAME_$JOB_ID.ERR
>
> # configuration
>
> . ~/.bash_profile
>
> #set
>
> module purge
> module add amber/gnu/11.0
> module add python/2.6.6
> export DO_PARALLEL=yes
>
> #HOSTFILE=$TMPDIR/sge_mpi_hostfile_openmpi
> #HOSTFILE=sge_mpi_hostfile_openmpi
> #echo "node191.aquarius2.storage slots=1" > ${HOSTFILE}
> #echo "node192.aquarius2.storage slots=1" >> ${HOSTFILE}
>
> PROGRAM=MMPBSA.py.MPI
> PROGRAM_OPTIONS=" -O -o -i mmpbsa.in dlta_G_3.dat -sp complex_solv.prmtop
> -cp complex.prmtop -rp receptor.prmtop -lp ligand.prmtop -y prod1.mdcrd.gz
> -make-mdins"
> mpirun --np 1 -x LD_LIBRARY_PATH -x PATH -x PYTHONPATH `which ${PROGRAM}`
> ${PROGRAM_OPTIONS}
>
> #############################################################
> #
>
> #set
>
> ##############################################################
>
>
>
> I choose cutres=10000. Then I submit the job using the same script but this
> time replacing -use-mdins with -use-mdins command . But still the
> calculation failed and I got the same error.
> This is the _MMPBSA_pb.mdin file after editing:
> File generated by MMPBSA.py
> &cntrl
> ntb=0, cut=999.0, ntpr=1, imin=5,
> maxcyc=0, igb=10, ipb=1, inp=1,
> /
> &pb
> dbfopt=1, epsin=1, epsout=80, istrng=100.0,
> radiopt=0, sprob=1.4, space=0.5, maxitn=1000,
> cavity_surften=0.00542, cavity_offset=-1.008,
> fillratio=4.0, cutres=10000
> /
>
> Please help me to fix this problem. Please find attached file (input +
> output file)
> Thanks
> Chanchal
>
> PS: I am using Amber-11
> _______________________________________________
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>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Tue Sep 21 2010 - 10:00:03 PDT
