Hi Jason,
Could you please tell me how to install iAPBS for Amber-11. The link you
have given me does not contain any instruction for amber 11. They have
provided installation guide for amber-9 & amber-10.
Thanks
Chanchal
On Wed, Sep 22, 2010 at 7:51 PM, Jason Swails <jason.swails.gmail.com>wrote:
> 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
> > > > _______________________________________________
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> > > > 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
> > > _______________________________________________
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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
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> > 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 Thu Sep 23 2010 - 08:30:08 PDT
