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

Marc Charendoff mcharend at sbcglobal.net
Thu Aug 10 05:52:56 CEST 2006

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 ]

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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