On Tue, Apr 30, 2013, Covington, Cody Lance wrote:
>
> Concerning improper dihedrals to preserve chirality.
> If I am using improper dihedrals in this way, then the atoms that make
> the angle are not necessarily bonded.
> I have read that LEaP will assign them based on the basis of the atoms
> being bonded to one another.
> Is there a way around this?
You question is not at all clear (at least to me). If you are adding your
own improper dihedral restraints (e.g. through the program makeCHIR_RST,
or by hand), this is done at the sander/pmemd stage and has nothing to do
with LEaP.
LEaP will add improper terms to atoms with exactly three bonds; this is
generally not what one wants for chirality (a chiral carbon would have four
bonds.)
If this doesn't help, we need more details. What do you mean by using
improper dihedrals in "this way", or "assign them" based on....? What exactly
did you try to do, and what was the problem you saw?
...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed May 01 2013 - 05:00:02 PDT
