On Fri, Feb 6, 2015 at 12:43 PM, Ahmet yıldırım <ahmedo...@gmail.com> wrote:
> Dear users, > > I get the following error when i use pdb2gmx tool of GROMACS 4.6.5, with > the AMBER99SB-ILDN ff. My command: > pdb2gmx -f protein.pdb -o protein.gro -p protein.top > > Fatal error: > In the chosen force field there is no residue type for 'LYS' as a > standalone (starting & ending) residue > > The pdb2gmx gives this error though terminal residues are prefixed with N > and C. > Maybe those prefixes are in the wrong columns of your input .pdb file. > Could there be something wrong with the input .pdb file? But i dont get > this error with another forcefield, 43a2. > GROMOS force fields handle termini differently from AMBER, so that's expected. Mark > > -- > Ahmet Yıldırım > -- > 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.
