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 $OUTPUT_DIR/prod1.mdcrd
Best,
Aldo
=======================================
Aldo Segura-Cabrera
Postdoctoral Fellow
Division of Experimental Hematology and Cancer Biology
Cancer and Blood Diseases Institute
Cincinnati Children's Hospital Medical Center
3333 Burnet Ave, MLC 7013, Cincinnati OH 45229
e-mail: Aldo.Segura-Cabrera.cchmc.org; aldosegura.gmail.com
=========================================
El Jueves, 27 de febrero, 2014 2:08:45, "hannes.loeffler.stfc.ac.uk" <hannes.loeffler.stfc.ac.uk> escribi�:
I would think the error message is very clear as to what is wrong.� You appear to have been using the parmtop file in place of the input coordinates and vice versa with pmemd (review what files you are supplying for -c and -p).� It's not a problem a problem with your LSF script.
Besides, if you are using the module system, why would you need to set MPI_ROOT, PATH and LD_LIBRARY_PATH by hand?� The whole point of having the module system is to have this done automatically.
Cheers,
Hannes.
________________________________________
From: Javier Alejandro Rendon Carrillo [biotecnologo.rendon.gmail.com]
Sent: 27 February 2014 06:05
To: AMBER Mailing List
Subject: Re: [AMBER] MMPBSA.py and entropy
im runing MMPBSA protocol like the tutorial i have a problem using
the production run.sh
this is the script:
#!/bin/bash
#BSUB -o %J.out
#BSUB -e %J.err
#BSUB -n 64
#BSUB -J amber_prod_in
#BSUB -q High
module load platform_mpi/platform_mpi-8.3.0
module load amber/amber_gcc
MPI_ROOT=/opt/platform_mpi; export MPI_ROOT
PATH=/opt/platform_mpi/bin:$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 Rend�n Carrillo
Laboratorio de Investigaci�n 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� desempe�o
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
cantidades de tiempo
M. Kant
A�o-1780
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Received on Thu Feb 27 2014 - 06:30:03 PST
