[gmx-users] Sorry, More on small molecule attempt...

[Tsjerk Wassenaar]

use grompp with the index file (grompp -n index.ndx)

On 8/10/06, Marc Charendoff <mcharend at sbcglobal.net> wrote:
> Hey All,
>
> Also, what is the correct way to coordinate results
> from make_ndx and the *.mdp variables "energygrps" and
> "xtc_grps"  to ensure grompp can reconcile between the
> two?
>
> Thanks for your patience.
>
>
>
>
> --- Marc Charendoff <mcharend at sbcglobal.net> wrote:
>
> > Date: Wed, 9 Aug 2006 20:52:56 -0700 (PDT)
> > From: Marc Charendoff <mcharend at sbcglobal.net>
> > Subject: More on small molecule attempt...
> > To: gmx-users at gromacs.org
> >
> > Hey all,
> >
> > I have learned to match up .itp file atom types to
> > the
> > proper force field when constructing a .gro, .top
> > pair
> > for grompp. However, I have now encountered another
> > stopping point. For given input:
> >
> > grompp -f minim.mdp -c AHLFIN.GRO -p topol.top -o
> > input.tpr
> >
> > I now get . .
> >
> > Back Off! I just backed up mdout.mdp to
> > ./#mdout.mdp.1#
> > checking input for internal consistency...
> > calling cpp...
> > processing topology...
> > Generated 1284 of the 1485 non-bonded parameter
> > combinations
> > Excluding 3 bonded neighbours for AHL   1
> > processing coordinates...
> > WARNING 1 [file "topol.top", line 8]:
> >   Bad box in file AHLFIN.GRO
> > Generated a cubic box    1.812 x    0.442 x    0.393
> > double-checking input for internal consistency...
> > renumbering atomtypes...
> > converting bonded parameters...
> > #      BONDS:   22
> > #     ANGLES:   27
> > #      PDIHS:   17
> > #      IDIHS:   5
> > #       LJ14:   26
> > initialising group options...
> > processing index file...
> > Analysing residue names:
> > Opening library file
> > /gromacs/share/gromacs/top/aminoacids.dat
> > There are:     1      OTHER residues
> > There are:     0    PROTEIN residues
> > There are:     0        DNA residues
> > Analysing Other...
> > Making dummy/rest group for T-Coupling containing 22
> > elements
> > Making dummy/rest group for Acceleration containing
> > 22
> > elements
> > Making dummy/rest group for Freeze containing 22
> > elements
> >
> -------------------------------------------------------
> > Program grompp, VERSION 3.3
> > Source code file: readir.c, line: 775
> >
> > Fatal error:
> > Group Protein not found in indexfile.
> > Maybe you have non-default goups in your mdp file,
> > while not using the '-n' option of grompp.
> > In that case use the '-n' option.
> >
> >
> -------------------------------------------------------
> >
> > My .top file looks like:
> >
> > #include "ffgmx.itp"
> > #include "AHLGMX.itp"
> >
> > [ system ]
> > AHL
> >
> > [ molecules ]
> > AHL   1
> >
> > What procedure do I need to follow for an index file
> > on a new molecule topology? Is it really needed? Are
> > there other items I am going to miss after this that
> > will keep me from a successful grompp run? Last, why
> > the "bad box file?" What did the Dundee Prodrg
> > server
> > (or more likely I) miss? Any guidance would be
> > appreciated. Am I getting any closer?
> >
> > Regards, Marc
> >
>
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-- 

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336