Hi Jonathan, The itp's for the ligands were given atomtype sections, but atomtypes (and other *types) may only be defined before any moleculetype definition (check chapter 5 of the manual for the topology format). You'll need to remove anything before the moleculetype directive from the itp files and make sure that all the atomtypes (and other *types) referred to are correct according to the listing in the force field.
Hope it helps, Tsjerk On Sun, Aug 4, 2013 at 8:46 AM, Jonathan Saboury <jsab...@gmail.com> wrote: > PDB file used :http://www.rcsb.org/pdb/explore.do?structureId=1cx2 > Commands used: http://pastebin.com/raw.php?i=YYG5ad7A > Compressed folder containing all files (10.2 MB): > http://www.sendspace.com/file/rka8ei > > So I want to simulate this complex. I am having problems with the .itp's > and do not know why. > > I get the error: > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Program grompp, VERSION 4.5.5 > Source code file: /build/buildd/gromacs-4.5.5/src/kernel/topio.c, line: 656 > > Fatal error: > Syntax error - File NAG_GMX.itp, line 3 > Last line read: > '[ atomtypes ]' > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > Here is the logic I used while trying to get teh simulation to work, please > let me know if this is correct, because there wasn't a tutorial example > like this. > > 1.) Separate the complexed pdb into teh standard residues and ligands, so > "ATOM", "HEM", "NAG" and "S58"in this case. > > 2.) There are multiple ligands in the pdb, so I need to delete all but one > molecule and create a forcefield .itp so I can include it in the .top file. > > 3.) Once the .itp's for the single molecules are created, you need to put > the complex back together. I was having problems with adding charges, so I > only added hydrogen’s to the ligands and created complex.pdb from the new > pdb files created from acpype. > > 4.) Minimize, relax waters, then simulate. > > So what did I do wrong here? Thanks!! :) > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Tsjerk A. Wassenaar, Ph.D. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists