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

[Marc Charendoff]

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
>