[gmx-users] converting L to D amino acid in the CHARMM force field in GROMACS where to alter dihedral
Mark.Abraham at anu.edu.au
Mon Mar 28 14:13:04 CEST 2011
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.
> On Sat, Mar 26, 2011 at 2:02 AM, Mark Abraham <Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at 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.
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users