Hi Jochen, If you're dealing with protein structures you can use multiprot: http://bioinfo3d.cs.tau.ac.il/MultiProt/
I put a runner for gromacs (do_multiprot) on the user contribution page some time ago, and can put up a more recent version if it doesn't work with GMX 3.3.3. Ran. Jochen Hub wrote: > Hi, > > I run frequently into the problem that I want to fit a structure on a > reference which is, however, not completely identical to the > structure. The reference could, e.g., have a different protonation > state or have an additional residue at a terminal. Is such a case a > backbone-fit using trjconv gets erroneous since the atomic numbers of > the backbone atoms in the two structures are not the same. > > The best solution would be the possiblity to give trjconv 2 index > files, one giving the N fit atoms of the reference and the other the N > related atoms (but with different atom numbers) of the fitted > structure. As far as I know, something like that is not supported by > gromacs so far, right? > > How do you usually deal with such a problem? Is there some more or > less easy workaround? > > By the way, removing the atoms that do not agree in the two structures > is not an option since I want to start a simulation from the fitted > structure. > > Thanks a lot, > Jochen > _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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
