Hello Chanchal,
Unfortunately, this appears to be an issue in PBSA, which I've encountered
several times myself. This error arises because there's not enough space
allotted to the PB pairlist, I believe. A PBSA developer may be able to
chime in here and shed some light on this. However, I couldn't find a
working solution to this problem even after hunting through the code for
awhile.
Another option in the meantime if you really want Poisson Boltzmann
solutions: you can always use sander.APBS instead, which uses the APBS
program to calculate PB contributions. Specifically, you need the iapbs
library to link sander to apbs. Detailed installation instructions can be
found here : http://mccammon.ucsd.edu/iapbs/ .
Hope this helps,
Jason
On Wed, Sep 22, 2010 at 1:41 PM, Chanchal <chanchal.kar.gmail.com> wrote:
> Hi Bill,
> As you mentioned, I changed the source code. I changed
> maxmax = ceiling(dble(natom)/2*dble(natom))
> to
> maxmax = ceiling(dble(natom)*dble(natom))
> in the pb_init.f file. I set the value cutres=10000 in _MMPBSA_pb.mdin.
> Still I got the same error (PB bomb in pb_reslist(): maxnbr too small).
> Please let me know how can I fix this error.
> Thanks
> Chanchal
>
> 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
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Sep 22 2010 - 11:00:05 PDT
