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Dear Amber Users,
I run into a problem when I am trying to analysis the entropy using Nmode in Amber7.0. The input file is much the same with the example from amber.
Do anybody have any suggestions?
%temp/amber7_bug/exe/mm_pbsa.pl mm_pbsa.in > mm_pbsa.log
Here is the error message,
Use ofuninitialized value at /local/etc/amber7/src/mm_pbsa/mm_pbsa_statistics.pm line 1259. Use of uninitialized value at/local/etc/amber7/src/mm_pbsa/mm_pbsa_statistics.pm line 1259. Use of
uninitialized value at /local/etc/amber7/src/mm_pbsa/mm_pbsa_statistics.pm
line 1259.Use of uninitialized value at
/local/etc/amber7/src/mm_pbsa/mm_pbsa_statistics.pm line 1259.
Here is mm_pbsa.log file,
=>> Init data
Presuming executables of amber suite to be in /local/etc/amber7/exe
=>> Reading input parameters
Found PREFIX => dna
Found PATH => ./selected/
Found COMPLEX => 0
Found RECEPTOR => 1
Found LIGAND => 0
Found RECPT => ./mtgtnowat.top
Found GC => 0
Found AS => 0
Found DC => 0
Found MM => 0
Found GB => 0
Found PB => 0
Found MS => 0
Found NM => 1
Found DIELC => 4
Found MAXCYC => 5000
Found DRMS => 0.1
Found DELPHI => /home/caiy/rotation_project/new/TGT/minustgt/delphi
=>> Checking sanity
Checking GENERAL
Checking NM =>> Creating input
Nmode input =>> Calculating energy / entropy contributions
Calc contrib for ./selected/dna_rec.crd.1
Minimize structure
Calc entropy =>> Doing statistics =>> Values of global variables
TEMP = 300
R = 8.314
gammaP = 0.00542
betaP = 0.92
gammaG = 0.0072
betaG = 0 =>> Reading input =>> Reordering files
Final order:
1. dna_rec.all.out: - =>> Reading files
Reading dna_rec.all.out
WARNING: Missing SROT for NM in 0 -> Taken from -1
WARNING: Missing STOT for NM in 0 -> Taken from -1
WARNING: Missing STRA for NM in 0 -> Taken from -1
WARNING: Missing SVIB for NM in 0 -> Taken from -1
=>> Treat special
parameters =>> Calc missing parameters =>> Calc average and stddev =>>
Print output to dna_statistics.out