That would mean that a new residue type will not be required? I just need the correct input D-coordinates?
On Sat, Mar 26, 2011 at 2:02 AM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > On 26/03/2011 2:27 AM, maria goranovic wrote: > > 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 ? > > > Unlike (say) AMBER's leap, pdb2gmx doesn't generate coordinates in a > general sense. It generates a topology that matches given coordinates, > fixing a few details as directed. It will fill valences with hydrogen atoms, > generate terminal groups, organize disulfides, and choose protonation states > of titratable residues, but it won't change geometries in the way you seem > to want. > > Neither does anything in the .top/.itp files stipulate the chirality of any > center (in all-atom models). Various dihedral angles change sign with > chirality, but the dihedral functions are all symmetric about the y-axis > (i.e. even). So I suspect you do not need to change anything about the > topology. Just use a molecule builder to change the chirality of the > relevant center in the input file to pdb2gmx. > > Mark > > > 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 > > > > -- > 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
