AMBER Archive (2003)

Subject: question about mm_pbsa?

From: Lishan Yao (yaolisha_at_pilot.msu.edu)
Date: Mon Mar 10 2003 - 10:04:17 CST

Hi:
   I try to decompose the interacation energy between solute and solvent. I get
some trouble. This is what I did:

=>> Init data
    Presuming executables of amber suite to be in /usr/local/amber7/exe

=>> Reading input parameters
    Found PREFIX => snapshot
    Found PATH => ./
    Found COMPLEX => 1
    Found RECEPTOR => 1
    Found LIGAND => 1
    Found COMPT => ./dhnp.prmtop
    Found RECPT => ./dhnp-wat.prmtop
    Found LIGPT => ./dhnp-now.prmtop
    Found GC => 0
    Found AS => 0
    Found DC => 1
    Found MM => 1
    Found GB => 0
    Found PB => 0
    Found MS => 0
    Found NM => 0
    Found DCTYPE => 2
    Found COMREC => 2-1218
    Found COMLIG => 1-1
    Found COMPRI => 1-1218
    Found RECRES => 1-1217
    Found RECPRI => 1-1217
    Found RECMAP => 2-1218
    Found LIGRES => 1-1
    Found LIGPRI => 1-1
    Found LIGMAP => 1-1
    Found DELPHI => /home/gohlke/src/delphi.98/exe.R10000/delphi

=>> Checking sanity
    Checking GENERAL
    Checking DC
    Checking MM

=>> Creating input
    Sander input

=>> Calculating energy / entropy contributions

=>> 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. snapshot_com.all.out: 1 - 1218
    2. snapshot_rec.all.out: 2 - 1218
    3. snapshot_lig.all.out: 1 - 1
=>> Reading files
    Reading snapshot_com.all.out
    Reading snapshot_rec.all.out
    Reading snapshot_lig.all.out
=>> Treat special parameters
=>> Calc missing parameters
    Processing MM BGAS
        Doing 1 MM BINT
Can't use an undefined value as an ARRAY reference at
/usr/local/amber7/src/mm_pbsa/mm_pbsa_statistics.pm line 1323.

  Please help!

Lishan