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

[Tsjerk Wassenaar]

Hi Marc,

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

Cheers,

Tsjerk

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
> 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
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>


-- 

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