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 <[EMAIL PROTECTED]> wrote: > Date: Wed, 9 Aug 2006 20:52:56 -0700 (PDT) > From: Marc Charendoff <[EMAIL PROTECTED]> > Subject: More on small molecule attempt... > To: gmx-users@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 > _______________________________________________ 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