Hi Alejandro,
I think you're using the "-p" and "-c" flags in a wrong way. -p should be associated with "complexwat.prmtop" and -c with "equil.rst". So, I think that this should be work (the same apply for the other runs: prod2, prod3...):
$MPI_ROOT/bin/mpirun -np 16 pmemd.MPI -O -i $OUTPUT_DIR/prod.in -o
$OUTPUT_DIR/prod1.out -p $INPUT_DIR/complexwat.prmtop -c
$OUTPUT_DIR/equil.rst -r \
$OUTPUT_DIR/prod1.rst -x $OUTPUT_DIR/prod1.mdcrd
Best,
Aldo
=======================================
Aldo Segura-Cabrera
Postdoctoral Fellow
Division of Experimental Hematology and Cancer Biology
Cancer and Blood Diseases Institute
Cincinnati Children's Hospital Medical Center
3333 Burnet Ave, MLC 7013, Cincinnati OH 45229
e-mail: Aldo.Segura-Cabrera.cchmc.org; aldosegura.gmail.com
=========================================
El Jueves, 27 de febrero, 2014 2:08:45, "hannes.loeffler.stfc.ac.uk" <hannes.loeffler.stfc.ac.uk> escribió:
I would think the error message is very clear as to what is wrong. You appear to have been using the parmtop file in place of the input coordinates and vice versa with pmemd (review what files you are supplying for -c and -p). It's not a problem a problem with your LSF script.
Besides, if you are using the module system, why would you need to set MPI_ROOT, PATH and LD_LIBRARY_PATH by hand? The whole point of having the module system is to have this done automatically.
Cheers,
Hannes.
________________________________________
From: Javier Alejandro Rendon Carrillo [biotecnologo.rendon.gmail.com]
Sent: 27 February 2014 06:05
To: AMBER Mailing List
Subject: Re: [AMBER] MMPBSA.py and entropy
im runing MMPBSA protocol like the tutorial i have a problem using
the production run.sh
this is the script:
#!/bin/bash
#BSUB -o %J.out
#BSUB -e %J.err
#BSUB -n 64
#BSUB -J amber_prod_in
#BSUB -q High
module load platform_mpi/platform_mpi-8.3.0
module load amber/amber_gcc
MPI_ROOT=/opt/platform_mpi; export MPI_ROOT
PATH=/opt/platform_mpi/bin:$PATH; export PATH
LD_LIBRARY_PATH=/opt/platform_mpi/lib:$LD_LIBRARY_PATH ; export
LD_LIBRARY_PATH
INPUT_DIR=/home/uanl/javier.rendon/Amber/MMPBSA/COMPLEX1
OUTPUT_DIR=/scratch/javier.rendon/COMPLEX1
$MPI_ROOT/bin/mpirun -np 16 pmemd.MPI -O -i $OUTPUT_DIR/prod.in -o
$OUTPUT_DIR/prod1.out -c $INPUT_DIR/complexwat.prmtop -p
$OUTPUT_DIR/equil.rst -r \
$OUTPUT_DIR/prod1.rst -x $OUTPUT_DIR/prod1.mdcrd
$MPI_ROOT/bin/mpirun -np 16 pmemd.MPI -O -i $OUTPUT_DIR/prod.in -o
$OUTPUT_DIR/prod2.out -c $INPUT_DIR/complexwat.prmtop -p
$OUTPUT_DIR/prod1.rst -r \
$OUTPUT_DIR/prod2.rst -x $OUTPUT_DIR/prod2.mdcrd
$MPI_ROOT/bin/mpirun -np 16 pmemd.MPI -O -i $OUTPUT_DIR/prod.in -o
$OUTPUT_DIR/prod3.out -c $INPUT_DIR/complexwat.prmtop -p
$OUTPUT_DIR/prod2.rst -r \
$OUTPUT_DIR/prod3.rst -x $OUTPUT_DIR/prod3.mdcrd
$MPI_ROOT/bin/mpirun -np 16 pmemd.MPI -O -i $OUTPUT_DIR/prod.in -o
$OUTPUT_DIR/prod4.out -c $INPUT_DIR/complexwat.prmtop -p
$OUTPUT_DIR/prod3.rst -r \
$OUTPUT_DIR/prod4.rst -x $OUTPUT_DIR/prod4.mdcrd
gzip -9 $OUTPUT_DIR/prod*.mdcrd
and the output prod1.out looks like
[-O]verwriting output
File Assignments:
| MDIN: prod.in
| MDOUT: prod1.out
*| INPCRD: complexwat.prmtop *
| PARM: equil.rst
| RESTRT: prod1.rst
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: prod1.mdcrd
| MDINFO: mdinfo
|LOGFILE: logfile
| ERROR: Could not read second line of
/home/uanl/javier.rendon/Amber/MMPBSA/COMPLEX1/complexwat.prmtop
| Bad inpcrd file!
what´s the problem in the script?
--
LBG Javier Alejandro Rendón Carrillo
Laboratorio de Investigación y Desarrollo
Tel. (044) 81-80-52-05-76
El control del espacio y el estricto manejo
del tiempo son factores determinantes
para aquellas personas que pretendan
alcanzar y sostener un desempeño
eficiente.
CONTROL DEL ESPACIO: Orden en las
cosas, en los archivos y en los registros.
ESTRICTO MANEJO DEL TIEMPO: Ser
puntual y saber fijar prioridades y
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Received on Thu Feb 27 2014 - 06:30:03 PST
