Hi Henry, Apparently NPCA is not listed as being protein, so pdb2gmx assumes that the chain begins with GLY. Add NPCA to the file residuetypes.dat one directory up, with the designation 'Protein'. I think that should solve it.
Groetjes, Tsjerk On Thu, Nov 24, 2011 at 6:59 PM, Henry Hocking <h.g.hock...@uu.nl> wrote: > Thank you Tsjerk, > I am now trying with amber99.ff but have encountered the following problem: > My PCA is at the N-terminus. I have an entry for [ NPCA ] in aminoacids.rtp > and have updated aminoacids.r2b to include NPCA and I've even added an entry > in aminoacids.hdb for NPCA. Yet when I generate my itp/gro files using > pdb2gmx, the NPCA is recognises (all atoms are there) but the second residue > [ GLY ] is now changed to [ NGLY ] in the itp file despite still being the > second residue in the gro file. As a test, if I remove NGLY from > aminoacids.r2b it complains that 'there is no residue type for 'GLY' as a > starting terminus' thus ignoring that the first residue of my chain is in > fact NPCA. > What could be going on here? The -ter flag has no effect here as I noticed > that for all amber99XX.ff the aminoacids.n.tdb files are empty. > Cheers, > Henry > > > > On 22 Nov 2011, at 18:17, Tsjerk Wassenaar wrote: > > Hi Henry, > > That would be a bit of a wild west approach. A better approximation > would be taking the charges from the backbone amide group, as it is > just an amide with on either side aliphatic carbons. Doing it properly > is a bit more involved, as for the G53a6 FF you need to choose > parameters giving the right free enthalpy of solvation. > > Groetjes, > > Tsjerk > > On Tue, Nov 22, 2011 at 5:10 PM, Henry Hocking <h.g.hock...@uu.nl> wrote: > > Dear all, > > Where can I find gromos53a6.ff parameters for pyroglutamate (PCA/ PGLU/ PGA) > > ? > > Alternatively, given that I have them in amber99.ff and oplsaa.ff is there a > > way I could adapt these to gromos53a6.ff? > > Can I use, for example, the gromos53a6.ff atom types from glutamine, > > add/remove appropriate bonds / angles / impropers and then take the > > corresponding charge values from my amber99.ff/aminoacid.rtp file. I assume > > that what I've just suggested is the cowboy method and that in reality it is > > not that straightforward, right? > > Kind regards, > > Henry > > -------------------------------------------------------- > > Henry Hocking, PhD > > Utrecht University > > Bijvoet Center for Biomolecular Research > > Padualaan 8 > > 3584 CH Utrecht, The Netherlands > > Phone: +31-30-2532875 > > Fax: +31-30-253 7623 > > E-mail: h.g.hock...@uu.nl > > > > > > -- > > 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 > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > post-doctoral researcher > Molecular Dynamics Group > * Groningen Institute for Biomolecular Research and Biotechnology > * Zernike Institute for Advanced Materials > University of Groningen > The Netherlands > -- > 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 > > -------------------------------------------------------- > Henry Hocking, PhD > Utrecht University > Bijvoet Center for Biomolecular Research > Padualaan 8 > 3584 CH Utrecht, The Netherlands > Phone: +31-30-2532875 > Fax: +31-30-253 7623 > E-mail: h.g.hock...@uu.nl > > > > > > -- > 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 > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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
