Dear Gromacs users, I am going to run a MD of a 20-residue protein which is phosphorylated on the Serine and Threonine residues with AMBER ff99SB-ILDN force field using Gromacs5.0. When I run gmx pdb2gmx and choose AMBER ff99SB-ILDN force field, it appears: fatal error: residues SEP not found in residue topology database.
I search some papers, and they say that we need to add add force fields parameters for the phosphorylated amino acids to the force filed parameter files. But I do not know how to add force fields parameters for the phosphorylated amino acids. Could anyone knows how to construct a model for the phosphorylated protein? Best regards, Ouyang. -- 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.
