Hi, I'm trying to run a simulation of a protein:ligand complex using chamm27 and cgenff2b7. After a little hacking (I'm using a PRES), I've used charmm2gromacs-pvm.py to convert cgenff2b7 to cgenff2b7.ff/, and then combined that with the charmm27 forcefield that comes with gromacs.
pdb2gmx runs without error, however when I run grompp, I get this: >Program grompp, VERSION 5.0.4 >Source code file: /var/tmp/portage/sci-chemistry/gromacs-5.0.4/work/gromacs-5.0.4/src/gromacs/gmxpreprocess/toppush.c, line: 742 > >Fatal error: >Unknown bond_atomtype CG1N1 > >For more information and tips for troubleshooting, please check the GROMACS >website at http://www.gromacs.org/Documentation/Errors I can't work out what bond_atomtype is, or exactly where I've been stupid. I've checked that: atomtypes.atp contains the following line >CG1N1 12.01100 ; for cyano group (if it's relevant, this was generated by appending the cgen atomtypes file to the charmm atomtypes file). ffcgenbonded.itp contains the following lines (under the [ bondtypes ] section) >CG1N1 CG2R61 1 0.1435 288696.0 >CG1N1 CG331 1 0.147 334720.0 >CG1N1 NG1T1 1 0.118 881150.4 charmm27cgen.ff/forcefield.itp contains >#include "ffcgenbonded.itp" topol.top contains >#include "./charmm27cgen.ff/forcefield.itp" grompp is being called with -p topol.top All bonds containing a CG1N1 atom in cgen.rtp are to one of the three atomtypes in ffcgenbonded.itp quoted above. Also, my ligand doesn't contain residues that have a CG1N1 atom in them (neither does my protein, surprise, surprise). So I don't know why it's looking at CG1N1, and I don't know why there are issues with this atomtype, and I don't know what a bond_atomtype is, which leaves me rather stuck. Does anybody have any suggestions? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
