Hi Gromacs folks, I want to simulation a protein complexed with a ligand. However, the protein covalently bonded with the ligand via N-C bond. The ligand has a size of 27 atoms. The solution I could think of now is to create a modified amino acid which includes both the amino acid side chain and the connected ligand in rtp and make modifications in ffbonded.itp accordingly.
I wonder if there is another route to get this done? Thanks, Ming -- 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.
