Dear Alan, if I completely understood how acpypi works, it seems that it generates the topology parameters from the pdb file of the molecule. But the problem is that I have the topology parameters (my angles, bond distances and dihedrals) and want to implement them in Gromacs, so actually I want to set specific parameters' values in gromacs.
Carla On Tue, Oct 20, 2009 at 5:16 PM, Alan <alanwil...@gmail.com> wrote: > Dear Carla, > > Let me suggest you the wikis at acpypi.googlecode.com. > > And then let me ask why amber94 and not amber99sb? And why not trying > acpypi in the link above as I guess it can do pretty much what you > want with much less pain? > > Cheers, > Alan > > On Tue, Oct 20, 2009 at 15:55, <gmx-users-requ...@gromacs.org> wrote: > > > > Hi everyone, > > I'm using the amber94 force field in gromacs. I need to add topology of a > > new molecule for my MD simulation. > > I saw this line "propers treated as RBs in GROMACS to use combine > multiple > > AMBER torsions per quartet" in my ffamber94bon.itp file. > > So it seems that I have to convert my proper dihedrals parameters into RB > > parameters, in order to run my simulation. > > Does anyone have an idea of how can I do this, to have the right > parameters > > for my molecule? > > > > Thanks a lot > > > > Carla > > -- > Alan Wilter Sousa da Silva, D.Sc. > PDBe group, PiMS project http://www.pims-lims.org/ > EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK > +44 (0)1223 492 583 (office) > _______________________________________________ > 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/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/mailing_lists/users.php >
_______________________________________________ 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/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/mailing_lists/users.php