HI all,
I am trying to run nmode using Amber 8. Initially I am trying to generate
the snapshots and then excute nmode. During the generation of the snapshots
it is giving me an error:
/home/mhb75/amber8_1/amber8/exe/make_crd_hg:
/home/mhb75/amber8_1/amber8/exe/make_crd_hg: cannot execute binary file
Close TO failed: -1/Broken pipe
The following is the .log file:
Init data
Presuming executables of amber suite to be in
/home/mhb75/amber8_1/amber8/exe
=>> Reading input parameters
Found PREFIX => snapshot
Found PATH => ./
Found COMPLEX => 1
Found RECEPTOR => 1
Found LIGAND => 1
Found COMPT => ./hAChE.prmtop
Found RECPT => ./hAChE-sarin.prmtop
Found LIGPT => ./MMB.prmtop
Found GC => 1
Found AS => 0
Found DC => 0
Found MM => 0
Found GB => 0
Found PB => 0
Found MS => 0
Found NM => 1
Found BOX => YES
Found NTOTAL => 67805
Found NSTART => 1
Found NSTOP => 5000
Found NFREQ => 200
Found NUMBER_LIG_GROUPS => 1
Found LSTART => 8263
Found LSTOP => 8295
Found NUMBER_REC_GROUPS => 1
Found RSTART => 1
Found RSTOP => 8262
Found DIELC => 4
Found MAXCYC => 10000
Found DRMS => 0.0001
Found TRAJECTORY => ./RES_md8.mdcrd
Found TRAJECTORY => ./RES_md9.mdcrd
Found TRAJECTORY => ./RES_md10.mdcrd
Found TRAJECTORY => ./RES_md11.mdcrd
Found TRAJECTORY => ./RES_md12.mdcrd
=>> Checking sanity
Checking GENERAL
Checking GC
Checking TRAJ
Checking NM
=>> Creating input
make_crd input
Nmode input
=>> Creating coordinates
Executing makecrd
Skipped title_line
Skipped title_line
Skipped title_line
Skipped title_line
The following is the pbs file
#PBS -l nodes=1:ppn=4
#PBS -q q16p192h
#PBS -l walltime=192:00:00
#PBS -r n
#PBS -V
cd $PBS_O_WORKDIR
cat $PBS_NODEFILE > job_nodes
mpdboot -n 1 -v -f $PBS_NODEFILE --rsh=rsh
mpiexec -n 1 /home/mhb75/amber8_1/amber8/exe/mm_pbsa.pl
extract_coordinate.mmpbsa > extract_coordinate.log
mpdallexit
Please give me some suggestions.
Thanks,
mani
-
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Received on Tue Jun 28 2011 - 15:00:04 PDT
