AMBER Archive (2006)

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

From: andy ng (andy810915_at_gmail.com)
Date: Fri Apr 07 2006 - 01:20:16 CDT

It worked when I put the number at the NUMBER_REC_GROUPS => 1, RSTART => 1
and RSTOP => 118 instead of the LIG.

On 4/7/06, andy ng <andy810915_at_gmail.com> wrote:
>
> 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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