Make a copy of the original Charm36.ff (to say, charmm36cgen.ff) then patch your cgenff conversion into it.
To keep things sane, I contained my cgenff conversion into its own ffbondedcgen.itp/ffnonbondedcgen.itp and included those .itps into the charmm36cgen.ff/forcefield.itp I also created separate cgen.rtp and cgen.hdb files and put them into charmm36cgen.ff as well. You've already figured out how to patch forcefields.dat so that's fine. On 2012-02-20 01:56:04PM +0800, Jernej Zidar wrote: > Hi. > Several months ago I was asking how to import and use two CHARMM > forcefields in Gromacs at the same time in MD simulations. The two > forcefields are CGENFF and CHARMM36. > > I was able to add the polymer monomers and relevant parameters so I > can now create a pair of top/gro files directly using the pdb2gmx > utility. I have also added some lipid molecules to the Gromacs version > of CHARMM36. > > I was able to solvate the CGENFF-generated compound using the command: > genbox -cp poly-1-1-1-1-1-new.gro -cs spc216.gro -p poly-1-1-1-1-1.top > -o wpoly-1-1-1-1-1.gro > > But I can't neutralize the system using the following command: > grompp -f em.mdp -c wpoly-1-1-1-1-1.gro -p wpoly-1-1-1-1-1.top -o ions.tpr > > To solve the problem I First tried including the spc.itp file from > CHARMM36 but that didn't work because of the missing atomtypes in > CGENFF's atomtypes.dat file. Oddly, adding the two missing atomtypes > to ./cgenff/atomtypes.dat didn't help: > Program grompp, VERSION 4.5.4 > Source code file: /build/buildd/gromacs-4.5.4/src/kernel/toppush.c, line: 1166 > > Fatal error: > Atomtype OW not found > > Then I tried to include the forcefield.itp from CHARMM36 + CHARMM36 > parameters for SPC water. Again it didn't help: > ERROR 1 [file forcefield.itp, line 1]: > Incorrect number of atomtypes for dihedral (0 instead of 2 or 4) > > ERROR 2 [file forcefield.itp, line 2]: > Incorrect number of atomtypes for dihedral (4 instead of 2 or 4) > > ERROR 3 [file forcefield.itp, line 3]: > Incorrect number of atomtypes for dihedral (4 instead of 2 or 4) > > ERROR 4 [file forcefield.itp, line 4]: > Incorrect number of atomtypes for dihedral (3 instead of 2 or 4) > > ERROR 5 [file forcefield.itp, line 5]: > Incorrect number of atomtypes for dihedral (4 instead of 2 or 4) > > ERROR 6 [file forcefield.itp, line 6]: > Incorrect number of atomtypes for dihedral (0 instead of 2 or 4) > > ------------------------------------------------------- > Program grompp, VERSION 4.5.4 > Source code file: /build/buildd/gromacs-4.5.4/src/kernel/topio.c, line: 668 > > Fatal error: > Syntax error - File forcefield.itp, line 13 > Last line read: > ' 1 2 yes 1.0 1.0' > Found a second defaults directive. > > I get NO errors if I do a minimization of my compund in vacuo only > using CGENFF. > > Could someone please advice what is the best course of action if one > wants to use CHARMM36 and CGENFF together in one simulation? > > Thanks in advance, > Jernej Zidar > -- > 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 -- ================================================================== Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- 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