how to select group numbers while running binding energy calculations
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Deep Bhattacharya
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Aug 12, 2016, 2:27:11 PM8/12/16
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I am trying to run calculation of binding energies using the parellel computing script This is the script that I have written #!/bin/sh #SBATCH --ntasks=16 #SBATCH --time=168:00:00 #SBATCH --mem-per-cpu=1024 #SBATCH --error=job.%J.err #SBATCH --output=job.%J.out module load compiler/gcc/4.8 openmpi/1.6 gromacs/4.6 export PATH=$WORK/apbs/bin:$WORK/deep1991/g_mmpbsa_p/bin:$PATH export APBS="mpirun -np $SLURM_NTASKS apbs" g_mmpbsa -f md.xtc -s md.tpr -i mmpbsa.mdp -n index.ndx -nomme -pbsa -decomp -pol polar.xvg -pcon contrib_pol.dat
But i am unable to select the group number and i get this error message ERROR 1 [file mmpbsa.mdp, line 130]: Invalid enum 'sp14' for variable srfm, using 'spl2' Next time use one of: 'spl2' 'spl4' 'mol' 'smol'
Reading file md.tpr, VERSION 4.6.5 (double precision) Reading file md.tpr, VERSION 4.6.5 (double precision) Group 0 ( System) has 45196 elements Group 1 ( Protein) has 1501 elements Group 2 ( Protein-H) has 1164 elements Group 3 ( C-alpha) has 149 elements Group 4 ( Backbone) has 447 elements Group 5 ( MainChain) has 597 elements Group 6 ( MainChain+Cb) has 737 elements Group 7 ( MainChain+H) has 741 elements Group 8 ( SideChain) has 760 elements Group 9 ( SideChain-H) has 567 elements Group 10 ( Prot-Masses) has 1501 elements Group 11 ( non-Protein) has 43695 elements Group 12 ( Other) has 80 elements Group 13 ( 4O4K) has 80 elements Group 14 ( NA) has 4 elements Group 15 ( Water) has 43611 elements Group 16 ( SOL) has 43611 elements Group 17 ( non-Water) has 1585 elements Group 18 ( Ion) has 4 elements Group 19 ( 4O4K) has 80 elements Group 20 ( NA) has 4 elements Group 21 ( Water_and_ions) has 43615 elements Group 22 ( Protein_4O4K) has 1581 elements Select a group: ------------------------------------------------------- Program g_mmpbsa, VERSION 4.6.7 Source code file: /home/rajendra/software/gromacs_source/gromacs-4.6.7/src/gmxlib/index.c, line: 1192
Fatal error: Cannot read from input For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors -------------------------------------------------------
Thanx for Using GROMACS - Have a Nice Day
Could you please help me solve this issue?
Sincerely,
Deep S Bhattacharya
Graduate Research Assistant
Mohs Biomedical Imaging &
Nanotechnology Group
Pharmaceutical Sciences
University of Nebraska Medical
Center
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Aug 16, 2016, 6:46:37 AM8/16/16
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