Hi Bill,
Thanks ! I have been abale to compile it.
Chanchal
On Fri, Sep 24, 2010 at 12:00 AM, Bill Miller III <brmilleriii.gmail.com>wrote:
> You will have to adjust these directions for Amber11, since the configure
> file is handled differently than previous versions of Amber. You should be
> able to replace
>
> cd $AMBERHOME/src
> ./configure_at icc
> ./configure_amber ifort
>
> with
>
> cd $AMBERHOME/AmberTools/src
> ./configure intel
>
> Of course, if you are using the gnu compilers with your installation of
> Amber, then you would replace 'intel' with 'gnu'. The rest of those
> instructions should be correct, though.
>
> Good luck!
>
> -Bill
>
>
>
> On Thu, Sep 23, 2010 at 5:51 PM, Chanchal <chanchal.kar.gmail.com> wrote:
>
> > Hi Jason,
> > The instruction for Amber-10 is as follows:
> >
> > export APBS_LIB=${APBS_PREFIX}/lib
> > cd $AMBERHOME/src
> > ./configure_at icc
> > ./configure_amber ifort
> > cd $AMBERHOME/src/sander
> > make clean
> > make depend
> > unset CC F77
> > unset CFLAGS FFLAGS LDFLAGS
> >
> > But I don't see neither configure_at nor configure_amber in the
> > directory $AMBERHOME/src for Amber-11. There is only config.h file in
> > $AMBERHOME/src .
> > And hence I am confused.
> > Thanks
> > Chanchal
> >
> >
> >
> > On Thu, Sep 23, 2010 at 5:15 PM, Jason Swails <jason.swails.gmail.com
> > >wrote:
> >
> > > 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
> > > > > > >
> > > > > > _______________________________________________
> > > > > > 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
> > > > > _______________________________________________
> > > > > 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
> > > _______________________________________________
> > > 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
> >
>
>
>
> --
> 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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Received on Fri Sep 24 2010 - 01:00:04 PDT
