I am facing a problem while simulating the tRNA molecule while converting pdb to gro, Fatal error: Atom OP3 in residue A 1 was not found in rtp entry RA5 with 31 atoms while sorting atoms.
force field used 3 (AMBER96 protein, nucleic AMBER94), water model TIP3P. i checked in gromacs error list, in that they mentioned simply re-name the atoms in your coordinate file<http://www.gromacs.org/Documentation/File_Formats/Coordinate_File> , how to rename the atom in coordinate file kindly give valuable suggestion how to rectify this error, Awaiting For your reply Thanking You -- 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
