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@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
