Yes, that would be the correct way to do this. I was hoping to take a shorter route, and just modifying a couple of dihedrals in the topology files output by pdb2gmx without having to make a new residue. Is that not possible at all ?
On Fri, Mar 25, 2011 at 12:24 PM, Tsjerk Wassenaar <tsje...@gmail.com>wrote: > Hi Maria, > > The general solution is to copy the entry in the .rtp file, modify the > dihedrals involved, and rename the entry to match the name used in the > coordinate (pdb) file. You may also need to copy the entries in the > .hdb file, as well as the .tdb files if it is a terminal residue. > > Hope it helps, > > Tsjerk > > On Fri, Mar 25, 2011 at 12:12 PM, maria goranovic > <mariagorano...@gmail.com> wrote: > > Hi > > Appreciate the quick help > > I am sorry, this is not an improper, but a proper dihedral that holds the > > chirality in place. Then the solution suggested by Meli would not work? I > do > > not have a D-ASP. I in fact have an L-ASP which i want to convert to D. > So > > the question is simply how to set the proper chirality to a D-amino acid > in > > CHARMM. > > > > > > Maria > > On Fri, Mar 25, 2011 at 11:49 AM, Tsjerk Wassenaar <tsje...@gmail.com> > > wrote: > >> > >> Hi Maria, > >> > >> The CHARMM force field is an all-atom one. That means it does not > >> require improper dihedrals to maintain chirality. If you have a D-ASP > >> in your structure file, you can rename it to ASP and just run pdb2gmx. > >> Mind not to regenerate hydrogens in that case, or make sure to modify > >> the hydrogen position for the D amino acids afterwards, to set the > >> proper chirality. > >> > >> Hope it helps, > >> > >> Tsjerk > >> > >> On Fri, Mar 25, 2011 at 11:09 AM, maria goranovic > >> <mariagorano...@gmail.com> wrote: > >> > Hello List > >> > I want to change an ASP to a D-ASP. I think it should be possible by > >> > simply > >> > changing 2 improper values around the chiral carbon to their opposite > >> > sign. > >> > Instead of making a brand new residue, I thought I would take the > >> > topology > >> > of an ASP generated by pdb2gmx, and simply change values manually in > the > >> > resulting .itp. However, this is not possible because gromacs wants to > >> > read > >> > the dihedral parameters from the ffbonded.itp file. Is it possible for > >> > me to > >> > explicitly state the parameters for these two dihedrals in my > d-asp.itp > >> > file? This will be the fastest solution to the problem because it > >> > precludes > >> > making a new residue or defining new atoms types and so on. With the > >> > CHARMM > >> > force field, I am not sure how q0 cq translate to c0 c1 c2 and c3 > which > >> > we > >> > are used to for gromos topologies. > >> > The mailing list search function was down, so I could not explore > prior > >> > messages about this. > >> > -- > >> > Maria > >> > > >> > -- > >> > Maria G. > >> > Technical University of Denmark > >> > Copenhagen > >> > > >> > -- > >> > 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 > > > > > > > > -- > > Maria G. > > Technical University of Denmark > > Copenhagen > > > > -- > > 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 > -- Maria G. Technical University of Denmark Copenhagen
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