On Thu, May 16, 2013 at 12:37 PM, Alan <alanwil...@gmail.com> wrote: > With ACPYPE I can convert any Amber *.prmtop and *.crd to Gromacs, but it > doesn't mean it will work straightforward (but I am working for that). > > For example, I am wondering how Gromacs team will port the Amber FF12SB, >
There's no plan to do so, but if someone wants to do so and can demonstrate they've done it correctly (e.g. suitable agreement with the native version) then contributions are always welcome. > since now we have atom types like '2C', '3C' (ie. starting with a number), > and GMX top won't accept this. > What is the specific issue? Of course, a simple solution is to do '2C' -> 'a2C' for example (and that > works with grompp 4.6.1), but I am wondering what GMX developers would do > here first, since using 3-letters wouldn't be a nice style. > Offhand, I can't think of a good reason to require an atom type to start with a letter, but there are a lot of hidden gotchas about how GROMACS parse lots of ugly file formats under lots of conditions... I am about to implement this workaround for ACPYPE, but just checking first > if someone has a better idea/suggestion. > Seems OK to me, offhand, but I don't have anything like full information, or time to get it :-( Mark > > Alan > > -- > Alan Wilter SOUSA da SILVA, DSc > Bioinformatician, UniProt - PANDA, EMBL-EBI > CB10 1SD, Hinxton, Cambridge, UK > +44 1223 49 4588 > -- > 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 > -- 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