AMBER Archive (2006)

Subject: AMBER: NGL error when creating snapshots for MM/PB(GB)SA

From: andy ng (andy810915_at_gmail.com)
Date: Fri Apr 07 2006 - 01:05:50 CDT

Dear amber user,

I'm trying to calculate binding energy using 3 trajectories. I managed to
calculate for complex and protein, but the peptide's one complaint about the
NGL when I trying to create snapshots of it. My peptide has 118 atoms and
the total atom numbers is 6031 from the prmtop file, and the md simulation
only contains this peptide with 10A water box. What could be wrong?

=>> Init data
    Presuming executables of amber suite to be in /usr/local/amber8//exe

=>> Reading input parameters
    Found PREFIX => pinA
    Found PATH => ./snapshots_5/
    Found COMPLEX => 0
    Found RECEPTOR => 0
    Found LIGAND => 1
    Found COMPT => ./complex.prmtop
    Found RECPT => ./protein.prmtop
    Found LIGPT => ./peptide.prmtop
    Found GC => 1
    Found AS => 0
    Found DC => 0
    Found MM => 0
    Found GB => 0
    Found PB => 0
    Found MS => 0
    Found NM => 0
    Found BOX => YES
    Found NTOTAL => 6031
    Found NSTART => 1
    Found NSTOP => 100
    Found NFREQ => 1
    Found NUMBER_LIG_GROUPS => 1
    Found LSTART => 1
    Found LSTOP => 118
    Found NUMBER_REC_GROUPS => 0
    Found RSTART => 0
    Found RSTOP => 0
    Found TRAJECTORY => ./peptide_md5.mdcrd
    Found DELPHI => /home/gohlke/src/delphi.98/exe.R10000/delphi

=>> Checking sanity
    Checking GENERAL
    Checking GC
    Checking TRAJ

=>> Creating input
    make_crd input

=>> Creating coordinates
    Executing makecrd

 Amber8 Module: make_crg_hg

 usage: make_crd_hg < trajectory_file

 Box info found: 42.9320000000000 42.9320000000000
   42.9320000000000
 Something wrong with NGL 0 118

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