On Thu, Dec 27, 2012 at 12:32 AM, Gert Peters <[email protected]> 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<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. 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 list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
