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
