Dear All,
I am trying to calculate entropy contribution of the protein using
ambe12 mmpbsa.pl script. The following is the input file.
.GENERAL
PREFIX snapshot
PATH ./
COMPLEX 0
RECEPTOR 1
LIGAND 0
RECPT ./hAChE.prmtop
GC 1
AS 0
DC 0
MM 0
GB 0
PB 0
MS 0
NM 1
.MAKECRD
BOX YES
NTOTAL 58507
NSTART 1
NSTOP 1000
NFREQ 1000
NUMBER_LIG_GROUPS 0
LSTART 0
LSTOP 0
NUMBER_REC_GROUPS 1
RSTART 1
RSTOP 8297
.NM
DIELC 4
MAXCYC 20000
DRMS 0.001
IGB 0
PROC 2
.TRAJECTORY
TRAJECTORY ./RES_md10.mdcrd
.PROGRAMS
The job is getting executed but nothing is written to the output and
the log file displaying the following error
=>> Doing statistics
=>> Reading input
=>> Reordering files
Final order:
1. snapshot_rec.all.out: -
=>> Reading files
Reading snapshot_rec.all.out
WARNING: Missing SROT for NM in 0 -> Taken from -1
For details see:
http://ambermd.org/Questions/mm_pbsa.html#check_completeness_missing_var_taken_from
WARNING: Missing STOT for NM in 0 -> Taken from -1
For details see:
http://ambermd.org/Questions/mm_pbsa.html#check_completeness_missing_var_taken_from
WARNING: Missing STRA for NM in 0 -> Taken from -1
For details see:
http://ambermd.org/Questions/mm_pbsa.html#check_completeness_missing_var_taken_from
WARNING: Missing SVIB for NM in 0 -> Taken from -1
For details see:
http://ambermd.org/Questions/mm_pbsa.html#check_completeness_missing_var_taken_from
=>> Values of parameters
TEMP = 300
R = 8.314
=>> Treat special parameters
Use of uninitialized value in multiplication (*) at
/usr/local/amber12/src/mm_pbsa/mm_pbsa_statistics.pm line 1457.
Use of uninitialized value in multiplication (*) at
/usr/local/amber12/src/mm_pbsa/mm_pbsa_statistics.pm line 1457.
Use of uninitialized value in multiplication (*) at
/usr/local/amber12/src/mm_pbsa/mm_pbsa_statistics.pm line 1457.
Use of uninitialized value in multiplication (*) at
/usr/local/amber12/src/mm_pbsa/mm_pbsa_statistics.pm line 1457.
=>> Calc missing parameters
=>> Calc average and stddev
=>> Print output to snapshot_statistics.out
=>> Print output (snap) to snapshot_statistics.out.snap
thanks,
mani
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Aug 01 2012 - 11:00:04 PDT
