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 <mailto: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
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