Hi Mark. >> How will pdb2gmx "know" it has to parse the monomeres.rtp file? >It can't. You must add to an existing .rtp file.
That's a problem (and a negative surprise), because I can't just add a new residue to the aminoacids.rtp in Charmm27.ff folder. Charmm27 and CGenFF are two different things, though they can be used together. >I will add that you will also have to add the residue to aminoacids.dat >file, so that the polymer repeat unit is recognized. for your small >polymer molecule you can just generate from the swissparam website That could well work in the case of the smallest polymer that is composed of just five monomers, but it is absolutely out of the question in the case of experimentally-relevant polymers that are composed of at least 40 units. Jernej -- 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
