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
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