Hi Steven I'm running simulations on DNA structures using the amber99sb-ildn FF. I had no problem generating .top and .gro files I might be able to help if you are interested. send me the PDB file.
Yocheved On Sun, Jan 20, 2013 at 10:57 PM, Tom <dna...@gmail.com> wrote: > Dear Gromacs User > > I built DNA with the pdb file and *mol2 > But when I used pdb2gmx to obtain *top file, pdb2gmx give error > report when I chose charmm27: > --------------------------- > Program pdb2gmx, VERSION 4.5.5 > Source code file: resall.c, line: 581 > Fatal error: > Residue 'T' not found in residue topology database > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > ------------------------------- > > Also can not work for the other forcefileds. > Why for simple DNA is so difficult to build topology file? > Is there any toolbox to help buld the top file? > > Thanks, > > Steven > -- > gmx-users mailing list gmx-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 > -- gmx-users mailing list gmx-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
