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 <[EMAIL PROTECTED]> 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
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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
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