The best way to find out is by looking at the dihedrals fpor the
aminoacid as defined by the forcefield. Someone may know it by heart,
but to make sure you need to check it yourself anway. It'll be hard to
defend your results before a picky referee by saying that "this dude on
a mailing list said so".
Erik
maria goranovic skrev 2011-03-29 11.51:
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
<mailto: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 <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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Maria G.
Technical University of Denmark
Copenhagen
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Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
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