[AMBER] Error in calculating MM-PBSA

From: Mustafa Alhaji Isa <mustafaisa.unimaid.edu.ng>
Date: Sun, 29 Oct 2017 13:41:59 +0530

Dear all,

I want to calculate the MM-PBSA using amber10, although when I used
the below command and input files, it display error msg

Input file for running PB and GB in serial
 endframe=2000, keep_files=2, interval=5, startframe=1,
 igb=2, saltcon=0.100,
 istrng=0.100, inp=1, radiopt=0,

#$ -cwd
#$ -S /bin/bash
#$ -e MMPBSA.dat
#$ -o nmode.err
source /etc/profile
export AMBERHOME=/opt/apps/amber/10/openmpi-mkl
/opt/mpi/openmpi/1.3.3/intel/bin/MMPBSA.py -O -i mmpbsa.in -o
MMPBSA.dat -sp com_solv.prmtop -cp complex.prmtop -rp receptor.prmtop
-lp ligand.prmtop –y prod.mdcrd

etc/profile: line 104: ulimit: open files: cannot modify limit:
Operation not permitted
/etc/profile: line 108: /usr/local/gaussian/g09/bsd/g09.profile: No
such file or directory
/opt/gridengine/default/spool/compute-0-25/job_scripts/5079464: line
8: /opt/mpi/openmpi/1.3.3/intel/bin/MMPBSA.py: No such file or

Warm regards
Mustafa Alhaji Isa
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Received on Sun Oct 29 2017 - 01:30:01 PDT
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