AMBER Archive (2003)

Subject: AMBER: Nmode Problem

From: Yuqin Cai (yc385_at_nyu.edu)
Date: Thu Nov 13 2003 - 10:26:25 CST

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

----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber@scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo@scripps.edu