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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Received on Fri Apr 07 2006 - 17:17:59 PDT
