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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Received on Tue Sep 21 2010 - 08:00:12 PDT
