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
_______________________________________________
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AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Sep 23 2010 - 15:30:04 PDT
