Hi, Short summary: Is there a gromacs version of the NAMD ApoA1 benchmark somewhere and if not, what tools can I use to convert CHARMM parameter/topology files to gromacs?
Now for the long version: I'm currently trying to "port" the popular ApoA1 benchmark used by NAMD and Desmond to gromacs. I have the input files for NAMD (they can be downloaded from http://www.ks.uiuc.edu/Research/namd/utilities/apoa1/), i.e. a PDB and PSF file as well as the corresponding .xplor force-field parameter files. I also have the underlying CHARMM topology files for the lipids involved. I've tried generating gromacs input files using pdb2gmx, using the CHARMM27 force-field therein. This doesn't work due to an "Atom OXT in residue GLN 243 was not found" error which seems to be an occurrence of bug #567 (http://redmine.gromacs.org/issues/567), yet it can't be circumvented by replacing the type of of the OT2 atom. I tried using the OPLS force field instead (after replacing HSD with HIS and other minor modifications in the .pdb), but this fails with the same error as above. If I don't include chain ids in the pdb, then it fails since it does not recognize the POPC lipid residues. I have the CHARMM topology files for these, but I have no idea how to convert these to gromacs topologies. Now, since the ApoA1 benchmark is quite popular, I'm assuming somebody might already have a gromacs version out there... Is this the case? If not, Is there some tool to convert CHARMM input, i.e. parameters and topologies, to gromacs? I've found and successfully used Mark Abraham's Perl script to convert the parameters. Therein he refers to a script by Yuguang Mu to convert topologies, which apparently used to be on the gromacs site (http://www.gromacs.org/@api/deki/files/76/=charmm_to_gromacs.tgz), but which seems to have disappeared. Many thanks and kind regards, Pedro Gonnet -- 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