Dear GMX experts, I am trying to prepare CHARMM36 parameter for non-standard amino acid using some instructions such as http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field and the user manual.
After I modified merged.rtp, merged.hdb, and residuetype.data files, gmxpdb2gmx successfully created gro, topol, and posre files. However, gmx grompp could not generate the tpr file because of several - maxwarn. The warmings commented as"duplicate atom index (34) in angles" and "duplicate atom index (34) in dihedrals". I think this kind error is related to the topology file especially I need to change ffbonded.itp of charmm36. However, I have no idea how to change this file. Could you explain to me how to fix this problem? Best regards -- 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 [email protected].
