Re: [AMBER] Error in calculating MM-PBSA

From: Elvis Martis <elvis.martis.bcp.edu.in>
Date: Sun, 29 Oct 2017 10:34:10 +0000

HI ,
Doesn't seem like an AMBER error.

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 >>> NOT an AMBER error
/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
directory >>> NOT a good place install AMBERTOOLS.

Consider upgrading to AMBERTOOLS17 (its free)
Install it in $HOME/AMBER16 >>> Follow installation instructions and to define environment variables.

Best Regards
Elvis Martis
Mumbai, INDIA.

________________________________________
From: Mustafa Alhaji Isa <mustafaisa.unimaid.edu.ng>
Sent: 29 October 2017 13:41
To: AMBER Mailing List
Subject: [AMBER] Error in calculating MM-PBSA

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
&general
 endframe=2000, keep_files=2, interval=5, startframe=1,
/
&gb
 igb=2, saltcon=0.100,
/
&pb
 istrng=0.100, inp=1, radiopt=0,
/

#!/bin/bash
#$ -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
directory

--
Warm regards
Mustafa Alhaji Isa
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Received on Sun Oct 29 2017 - 04:00:02 PDT
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