Thanks Bill !! I will try it today and let you know the outcome.
On Tue, Sep 21, 2010 at 6:44 PM, Bill Miller III <brmilleriii.gmail.com>wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Bill Miller III
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-6715
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Sep 21 2010 - 13:30:04 PDT
