Dear Vicente: If you can build your own hydrogen atom coordinates in your modified residue, then I suggest that you look at the lysine entry in the .rtp file in your force field directory, copy it, and modify it to match your modified amino acid. This will have a different location based on your force field, but for amber99 it would be here: share/gromacs/top/amber99.ff/aminoacids.rtp
Then, you need to modify share/gromacs/top/residuetypes.dat so that it includes your amino acid name as a Protein residue. That should allow you to run gmx pdb2gmx with an input of a regular protein structure and get a .itp file for your protein with the modified residue. If you need gromacs to add hydrogens for you, then that will require also modifying the forcefield .hdb file(s), but it sounds like you might already have that under control. Good luck, this is straightforward but reasonably tricky. Chris. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
