James Starlight wrote > > Dear Gromac's users! > > I'm working with the GFP protein which has chromophore (CRO) group > which is covalently bonded to the protein. I want to add new residue > to the Gromos 53.6 ff. by means of algorithm described here. > > > For that I've coppied files to my local work dirr and modify all of > them in accordance to the above tutorial- I've coppied .itp of CRO to > the aminoacids.rtp > > [ CRO ] > [ atoms ] > etc > > I've defined bonds of the djacent real amino acids in the specbond.dat
Seems dangerous from my memory of GFP. You should probably be making a single residue for the whole chromophore, in which case a model that does not need specbond.dat is possible. James Starlight wrote > > Finally I've defined CRO (as the protein) in the residuetypes.dat > > When I've try use pdb2gmx I've obtain error > > Fatal error: > Residue 'CRO' not found in residue topology database > > > What I've done wrong? > If http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database and its links don't help, you'll have to inspect carefully your output from pdb2gmx for clues. Mark -- View this message in context: http://gromacs.5086.n6.nabble.com/Adding-New-Residue-to-the-Gromos-53-6-ff-tp4999959p4999960.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
