Something is really weird about that system. The error message changes with the number of residues I use. Everything works fine for 2 and 3 residues. With 4 residues I get : ___________________________________________________________ Warning: Starting residue DUL1 in chain not identified as Protein/RNA/DNA. Warning: Starting residue DUL2 in chain not identified as Protein/RNA/DNA. Warning: Starting residue DUL3 in chain not identified as Protein/RNA/DNA. Warning: Starting residue DUL4 in chain not identified as Protein/RNA/DNA. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 11 out of 11 lines of specbond.dat converted successfully Special Atom Distance matrix: DUL1 DUL1 DUL1 DUL2 DUL2 DUL2 DUL3 DU01 DU12 DU23 DU04 DU15 DU26 DU07 DUL1 DU12 0.200 DUL1 DU23 0.346 0.200 DUL2 DU04 0.400 0.346 0.529 DUL2 DU15 0.529 0.400 0.529 0.200 DUL2 DU26 0.529 0.346 0.400 0.346 0.200 DUL3 DU07 0.400 0.600 0.721 0.693 0.872 0.916 DUL3 DU18 0.200 0.400 0.529 0.529 0.693 0.721 0.200 DUL3 DU29 0.200 0.346 0.400 0.600 0.721 0.693 0.346 DUL4 DU010 0.400 0.529 0.721 0.400 0.600 0.721 0.400 DUL4 DU111 0.346 0.400 0.600 0.200 0.400 0.529 0.529 DUL4 DU212 0.200 0.200 0.400 0.200 0.346 0.400 0.529 DUL3 DUL3 DUL4 DUL4 DU18 DU29 DU010 DU111 DUL3 DU29 0.200 DUL4 DU010 0.346 0.529 DUL4 DU111 0.400 0.529 0.200 DUL4 DU212 0.346 0.400 0.346 0.200 Linking DUL-1 DU0-1 and DUL-1 DU1-2... Linking DUL-1 DU0-1 and DUL-3 DU1-8... Linking DUL-1 DU0-1 and DUL-3 DU2-9... Linking DUL-1 DU0-1 and DUL-4 DU2-12... Linking DUL-1 DU1-2 and DUL-1 DU2-3... Linking DUL-1 DU1-2 and DUL-4 DU2-12... Linking DUL-2 DU0-4 and DUL-2 DU1-5... Linking DUL-2 DU0-4 and DUL-4 DU1-11... Linking DUL-2 DU0-4 and DUL-4 DU2-12... Linking DUL-2 DU1-5 and DUL-2 DU2-6... Linking DUL-3 DU0-7 and DUL-3 DU1-8... Linking DUL-3 DU1-8 and DUL-3 DU2-9... Linking DUL-4 DU0-10 and DUL-4 DU1-11... Linking DUL-4 DU1-11 and DUL-4 DU2-12... Segmentation fault (core dumped) ___________________________________________________________
and with 5 residues: ___________________________________________________________ inking DUL-1 DU0-1 and DUL-1 DU1-2... Linking DUL-1 DU0-1 and DUL-3 DU1-8... Linking DUL-1 DU0-1 and DUL-3 DU2-9... Linking DUL-1 DU0-1 and DUL-4 DU2-12... Linking DUL-1 DU1-2 and DUL-1 DU2-3... Linking DUL-1 DU1-2 and DUL-4 DU2-12... Linking DUL-2 DU0-4 and DUL-2 DU1-5... Linking DUL-2 DU0-4 and DUL-4 DU1-11... Linking DUL-2 DU0-4 and DUL-4 DU2-12... Linking DUL-2 DU0-4 and DUL-5 DU2-15... Linking DUL-2 DU1-5 and DUL-2 DU2-6... Linking DUL-2 DU1-5 and DUL-5 DU2-15... Linking DUL-3 DU0-7 and DUL-3 DU1-8... Linking DUL-3 DU1-8 and DUL-3 DU2-9... Linking DUL-4 DU0-10 and DUL-4 DU1-11... Linking DUL-4 DU1-11 and DUL-4 DU2-12... Linking DUL-5 DU0-13 and DUL-5 DU1-14... Linking DUL-5 DU1-14 and DUL-5 DU2-15... Opening force field file /home/swacker/System/gromacs/GMX46/amber99sb-ildn.ff/aminoacids.arn Opening force field file /home/swacker/System/gromacs/GMX46/amber99sb-ildn.ff/dna.arn Opening force field file /home/swacker/System/gromacs/GMX46/amber99sb-ildn.ff/rna.arn Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 5 residues with 15 atoms Making bonds... ------------------------------------------------------- Program gmx pdb2gmx, VERSION 5.1-dev-20140607-3db1d85 Source code file: /home/swacker/Install_Software/gromacs/src/gromacs/gmxpreprocess/pgutil.c, line: 125 Fatal error: Residue 1 named DUL of a molecule in the input file was mapped to an entry in the topology database, but the atom used in an interaction of type special bond in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. ___________________________________________________________ my specbonds.dat: ___________________________________________________________ 11 CYS SG 1 CYS SG 1 0.2 CYS2 CYS2 CYS SG 1 HEM FE 2 0.25 CYS2 HEME CYS SG 1 HEM CAB 1 0.18 CYS2 HEME CYS SG 1 HEM CAC 1 0.18 CYS2 HEME HIS NE2 1 HEM FE 1 0.2 HIS1 HEME MET SD 1 HEM FE 1 0.24 MET HEME CO C 1 HEME FE 1 0.19 CO HEME CYM SG 1 CYM SG 1 0.2 CYS2 CYS2 DUL DU0 4 DUL DU1 4 0.2 DUL DUL DUL DU0 4 DUL DU2 4 0.2 DUL DUL DUL DU1 4 DUL DU2 4 0.2 DUL DUL ___________________________________________________________ example.pdb ___________________________________________________________ TITLE PMX MODEL REMARK THIS IS A SIMULATION BOX CRYST1 36.770 36.770 36.770 90.00 90.00 90.00 P 1 1 MODEL 1 ATOM 1 DU0 DUL L 1 16.653 16.052 18.385 1.00 0.00 ATOM 2 DU1 DUL L 1 14.921 17.052 18.385 1.00 0.00 ATOM 3 DU2 DUL L 1 13.189 16.052 18.385 1.00 0.00 ATOM 4 DU0 DUL L 2 16.653 20.052 18.385 1.00 0.00 ATOM 5 DU1 DUL L 2 14.921 21.052 18.385 1.00 0.00 ATOM 6 DU2 DUL L 2 13.189 20.052 18.385 1.00 0.00 ATOM 7 DU0 DUL L 3 20.117 14.052 18.385 1.00 0.00 ATOM 8 DU1 DUL L 3 18.385 15.052 18.385 1.00 0.00 ATOM 9 DU2 DUL L 3 16.653 14.052 18.385 1.00 0.00 ATOM 10 DU0 DUL L 4 20.117 18.052 18.385 1.00 0.00 ATOM 11 DU1 DUL L 4 18.385 19.052 18.385 1.00 0.00 ATOM 12 DU2 DUL L 4 16.653 18.052 18.385 1.00 0.00 ATOM 13 DU0 DUL L 5 20.117 22.052 18.385 1.00 0.00 ATOM 14 DU1 DUL L 5 18.385 23.052 18.385 1.00 0.00 ATOM 15 DU2 DUL L 5 16.653 22.052 18.385 1.00 0.00 ATOM 16 DU0 DUL L 6 23.581 16.052 18.385 1.00 0.00 ATOM 17 DU1 DUL L 6 21.849 17.052 18.385 1.00 0.00 ATOM 18 DU2 DUL L 6 20.117 16.052 18.385 1.00 0.00 ATOM 19 DU0 DUL L 7 23.581 20.052 18.385 1.00 0.00 ATOM 20 DU1 DUL L 7 21.849 21.052 18.385 1.00 0.00 ATOM 21 DU2 DUL L 7 20.117 20.052 18.385 1.00 0.00 ___________________________________________________________ aminoacids.rtp entry: ___________________________________________________________ [ DUL ] [ atoms ] DU0 DUM 0.000 1 DU1 DUM 0.000 2 DU2 DUM 0.000 3 ___________________________________________________________ -- 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.