Hello,
It should work the same way.
Good luck!
Jason
On Thu, Sep 23, 2010 at 11:10 AM, Chanchal <chanchal.kar.gmail.com> wrote:
> 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
> > > > > _______________________________________________
> > > > > 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
> > > >
> > > _______________________________________________
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> > > 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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>
--
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 - 08:30:11 PDT
