Just curious, this would also hold true for the OPLA-AA force field. It is all-atom, so no changes seems to be necessary besides making a d-amino acid in the input ?
On Mon, Mar 28, 2011 at 2:13 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > On 28/03/2011 8:45 PM, maria goranovic wrote: > > That would mean that a new residue type will not be required? I just need > the correct input D-coordinates? > > > Try it, before asking about it :-) I said "I suspect you do not need to > change anything about the topology", but I haven't actually done anything > like this ever. Topologies and code shouldn't care about chirality, so you > shouldn't need to do anything other than input the configuration you want. > > Mark > > > 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 >> > > > -- > 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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