[gmx-users] Dangling bond at terminal end of RNA rosetta model
Hi everybody, Im trying to use GROMACS for MD of a RNA model generated by Rosetta (FARFAR). As a test I try processing a modelledpdb file. When I prepare thetopology files (pdb2gmx -f test.pdb -ff amber99 -ignh ) from pdb I encounter following output : Sorting it all out... Opening force field file /usr/local/gromacs/share/gromacs/top/amber99.ff/aminoacids.hdb Opening force field file /usr/local/gromacs/share/gromacs/top/amber99.ff/dna.hdb Opening force field file /usr/local/gromacs/share/gromacs/top/amber99.ff/rna.hdb Opening force field file /usr/local/gromacs/share/gromacs/top/amber99.ff/aminoacids.n.tdb Opening force field file /usr/local/gromacs/share/gromacs/top/amber99.ff/aminoacids.c.tdb Back Off! I just backed up topol.top to ./#topol.top.12# Processing chain 1 'A' (165 atoms, 8 residues) Identified residue rG1 as a starting terminus. Identified residue rC8 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully --- Program pdb2gmx, VERSION 4.5.5 Source code file: pdb2top.c, line: 1031 Fatal error: There is a dangling bond at at least one of the terminal ends and the force field does not provide terminal entries or files. Edit a .n.tdb and/or .c.tdb file. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- When processing the corresponding structure from the pdb database (2IXZ)all files are generated as expected. I tried to compare the de novo model with the experimentally determined one but I cant find the problem(all terminal residues seem to have the same amountof atoms when ignoring the hydrogen atoms). I dont have a clue where to look next. Anyone got a clueto solve this issue? Thanks in advance, Kind regards, Gert -- gmx-users mailing listgmx-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
Re: [gmx-users] Dangling bond at terminal end of RNA rosetta model
On 12/26/12 6:32 PM, Gert Peters wrote: Hi everybody, Im trying to use GROMACS for MD of a RNA model generated by Rosetta (FARFAR). As a test I try processing a modelledpdb file. When I prepare thetopology files (pdb2gmx -f test.pdb -ff amber99 -ignh ) from pdb I encounter following output : Sorting it all out... Opening force field file /usr/local/gromacs/share/gromacs/top/amber99.ff/aminoacids.hdb Opening force field file /usr/local/gromacs/share/gromacs/top/amber99.ff/dna.hdb Opening force field file /usr/local/gromacs/share/gromacs/top/amber99.ff/rna.hdb Opening force field file /usr/local/gromacs/share/gromacs/top/amber99.ff/aminoacids.n.tdb Opening force field file /usr/local/gromacs/share/gromacs/top/amber99.ff/aminoacids.c.tdb Back Off! I just backed up topol.top to ./#topol.top.12# Processing chain 1 'A' (165 atoms, 8 residues) Identified residue rG1 as a starting terminus. Identified residue rC8 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully --- Program pdb2gmx, VERSION 4.5.5 Source code file: pdb2top.c, line: 1031 Fatal error: There is a dangling bond at at least one of the terminal ends and the force field does not provide terminal entries or files. Edit a .n.tdb and/or .c.tdb file. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- When processing the corresponding structure from the pdb database (2IXZ)all files are generated as expected. I tried to compare the de novo model with the experimentally determined one but I cant find the problem(all terminal residues seem to have the same amountof atoms when ignoring the hydrogen atoms). I dont have a clue where to look next. Anyone got a clueto solve this issue? The most common issue is residue name. Terminal nucleic acids are named, e.g., RG5 to indicate 5' terminus. Similarly, RG is an internal residue and RG3 is a 3' terminal residue. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-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
Re: [gmx-users] Dangling bond at terminal end of RNA rosetta model
On Thu, Dec 27, 2012 at 12:32 AM, Gert Peters gert.pet...@ugent.be wrote: Hi everybody, Im trying to use GROMACS for MD of a RNA model generated by Rosetta (FARFAR). As a test I try processing a modelledpdb file. When I prepare thetopology files (pdb2gmx -f test.pdb -ff amber99 -ignh ) from pdb I encounter following output : Sorting it all out... Opening force field file /usr/local/gromacs/share/** gromacs/top/amber99.ff/**aminoacids.hdb Opening force field file /usr/local/gromacs/share/** gromacs/top/amber99.ff/dna.hdb Opening force field file /usr/local/gromacs/share/** gromacs/top/amber99.ff/rna.hdb Opening force field file /usr/local/gromacs/share/** gromacs/top/amber99.ff/**aminoacids.n.tdb Opening force field file /usr/local/gromacs/share/** gromacs/top/amber99.ff/**aminoacids.c.tdb Back Off! I just backed up topol.top to ./#topol.top.12# Processing chain 1 'A' (165 atoms, 8 residues) Identified residue rG1 as a starting terminus. Identified residue rC8 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully --**- Program pdb2gmx, VERSION 4.5.5 Source code file: pdb2top.c, line: 1031 Fatal error: There is a dangling bond at at least one of the terminal ends and the force field does not provide terminal entries or files. Edit a .n.tdb and/or .c.tdb file. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/**Documentation/Errorshttp://www.gromacs.org/Documentation/Errors --**- When processing the corresponding structure from the pdb database (2IXZ)all files are generated as expected. I tried to compare the de novo model with the experimentally determined one but I cant find the problem(all terminal residues seem to have the same amountof atoms when ignoring the hydrogen atoms). I dont have a clue where to look next. AMBER parameterizes the terminal residues differently from the non-terminal residues. See rna.rtp. That requires that the terminal residues have a different residue name that pdb2gmx can match accordingly. With the information we have, nobody can say why one of your input files works and the other doesn't. Mark -- gmx-users mailing listgmx-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
