[gmx-users] More on small molecule attempt...
tsjerkw at gmail.com
Thu Aug 10 09:06:14 CEST 2006
In this case, the problem is in your .mdp file. In there you have a
reference to a group Protein, maybe i the comm_grps, the tc_groups or
possibly somewhere else. Since you don't have a protein, you have to
remove such references. If your system consists of AHL in solvent, you
can use AHL as a group for comm removal and probably System will be
best for temperature coupling
On 8/10/06, Marc Charendoff <mcharend at sbcglobal.net> wrote:
> 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
> I now get . .
> Back Off! I just backed up mdout.mdp to
> checking input for internal consistency...
> calling cpp...
> processing topology...
> Generated 1284 of the 1485 non-bonded parameter
> 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
> 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
> Making dummy/rest group for Acceleration containing 22
> Making dummy/rest group for Freeze containing 22
> 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 ]
> [ 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
9747AG Groningen, The Netherlands
+31 50 363 4336
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