here is a simple example (for more complex ones see the existing residues in an aminoacids.rtp)
assume molecule looks like A-B-C where the -'s are bonds with residues AAA, BBB, CCC containing the corresponding atoms, then the .rtp should contain something like: [ AAA ] [ atoms ] A typeA chargeA 1 [ bonds ] A +B [ BBB ] [ atoms ] B typeB chargeB 1 [ bonds ] B -A B +C [ CCC ] [ atoms ] C typeC chargeC 1 [ bonds ] C -B the + and - define which direction the connection should go I hope that's helpful Richard On Fri, 2012-05-11 at 15:43 +0100, Steven Neumann wrote: > Dear Gromacs Users, > > I created my own residues in aminoacids.rtp which each is formed of > one atom. I would like to somehow create bonds between then using > standart harmonic potential. Could you please advise how to do this? > > Stevem > -- > 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