On Wednesday 16 August 2006 23:43, Mark Abraham wrote: > Jerome Henin wrote: > > Hi all, > > > > As quite a few people have done before, I am about to try and convert a > > CHARMM topology into a GROMACS one. To that effect, I will probably need > > one or several programs that will do part of the job. When these are > > done, I suppose they might be of interest to others on this list. > > > > Since I am not keen on the idea of reinventing the wheel, I would like to > > know if there is an existing base I can build on. Have you guys been > > doing something of the sort? Using what tools? > > I have previously made available under GPL two perl scripts; one that > convert CHARMM parameter files into GROMACS parameter files (.itp), and > another that corrects the output of grompp to achieve correct treatment > of U-B terms, 1,4 LJ terms and multiple periodic dihedrals. The former > now works on a range of CHARMM parameter files. I attempted to update > the link on the GROMACS web page today, and it has disappeared, > presumably awaiting moderation. Please mail me off-list for a updated > copy if they don't appear in the next few days. There's no change to > their function, but the former script now accept a wider range of inputs. > > For residue topology (.rtf) files, you need to consult those of Yuguang > Mu, available here > http://www.gromacs.org/old/topologies/uploaded_force_fields/charmm_gromacs. >tar.gz
Thanks a lot for the info! I will try that. From what I see, there might be some work left on the residue topology conversion. > > A side question: does is sound reasonable to emulate Urey-Bradley angle > > potentials by adding an extra "bond" term? > > U-B angle potentials are implemented natively in GROMACS - see chapters > four and five in the manual. There are of course a few ways you could > hack an emulation of them. I have a problem with that, though. I did look in the manual, and Urey-Bradley potentials are mentioned in chapter 4, but I cannot see any reference to them in chapter 5. For instance, table 5.4 lists all bonded interactions, and none of the 3 angle potentials there is Urey-Bradley. But it seems that combining a harmonic angle with a harmonic potential (bonds, type 6) is a clean way of obtaining that result. Have I missed something? Thanks, Jerome _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
