Dear Gromacs users, I have obtained the error: "There is a dangling bond at at least one of the terminal ends...",
running pdb2gmx (4.6.5 version) with the command: pdb2gmx -f J.pdb -o J.gro -p J.top J.itp. PDB file 1BJ5 from RCSB was used; 'A' chain and five ligand molecules attached to it were taken, all heavy atoms restored and OXT atom added with SwissPDBViewer 4.00 to the C termini: ATOM 4652 OXT LEU A 585 -9.378 -4.234 37.788 1.00 99.99 To avoid "dangling bond" error I tried both N- and C- terminii special residues as follows: ATOM 1 N NASPA 1 57.277 12.540 12.230 1.00 99.99 or ATOM 1 N NASP A 1 57.277 12.540 12.230 1.00 99.99 This yielded new error instead: "residue 'HISE' not found in residue topology database" (But I really haven't such residue name in my PDB!) I use self-made force field combined from GAFF parameters for ligands, AMBER99 for protein and tip3p for water, however I already succesfully perfomed modeling of the same pdb with the same force field by 4.5.3 version. Could you, please, help me? Best regards, Igor Shchechkin -- 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.