[gmx-users] maximum number of specbonds?
Hi, I am parameterizing an artifical ligand. I use small residue-like fragments and connect them with specbonds in a grid, since I need arbitrary shapes and sizes. Now, I ran into segmentation faults, when the grid becomes to large. Is there an upper limit for the specbonds? How can I fix that or do you see a better way to solve that issue? Thanks Soren -- 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.
Re: [gmx-users] maximum number of specbonds?
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: DUL1DUL1DUL1DUL2DUL2DUL2DUL3 DU01DU12DU23DU04DU15DU26DU07 DUL1DU12 0.200 DUL1DU23 0.346 0.200 DUL2DU04 0.400 0.346 0.529 DUL2DU15 0.529 0.400 0.529 0.200 DUL2DU26 0.529 0.346 0.400 0.346 0.200 DUL3DU07 0.400 0.600 0.721 0.693 0.872 0.916 DUL3DU18 0.200 0.400 0.529 0.529 0.693 0.721 0.200 DUL3DU29 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 DUL3DUL3DUL4DUL4 DU18DU29 DU010 DU111 DUL3DU29 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 CYS2CYS2 CYS SG 1 HEM FE 2 0.25CYS2HEME CYS SG 1 HEM CAB 1 0.18CYS2HEME CYS SG 1 HEM CAC 1 0.18CYS2HEME HIS NE2 1 HEM FE 1 0.2 HIS1HEME MET SD 1 HEM FE 1 0.24MET HEME CO C 1 HEMEFE 1 0.19CO HEME CYM SG 1 CYM SG 1 0.2 CYS2CYS2 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
Re: [gmx-users] maximum number of specbonds?
Hi, It sounds like your practical options are to build some larger fragments to use when required, or generate your topology with something else, e.g. a custom script. pdb2gmx was built with slightly-branched polymers in mind, not much else. Mark On Thu, Jun 19, 2014 at 6:11 PM, Soren Wacker swac...@ucalgary.ca wrote: Hi, I am parameterizing an artifical ligand. I use small residue-like fragments and connect them with specbonds in a grid, since I need arbitrary shapes and sizes. Now, I ran into segmentation faults, when the grid becomes to large. Is there an upper limit for the specbonds? How can I fix that or do you see a better way to solve that issue? Thanks Soren -- 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. -- 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.
