On Tue, Feb 21, 2017 at 4:33 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> another option that may work better for a protein is to edit the PDB file,
> deleting all of the side chain atoms on this amino acid except the CA and
> HA. Then, change chirality by swapping the coordinates of these 2 atoms.
> Save and load it into Leap, which should rebuild any missing atoms. Of
> course it won't have an ideal conformation and may have steric clashes, but
> it's a starting point for minimization (and very careful checking of the
> results).
>
>
.Carlos: great, sounds like a good TODO feature for pdb4amber (that
integrates ParmEd, tleap and even do minimization for exactly what you said
:D).
https://github.com/hainm/pdb4amber-contrib/blob/master/images/trp_cage_minimization.gif
Hai
> On Tue, Feb 21, 2017 at 4:26 PM, Lachele Foley <lf.list.gmail.com> wrote:
>
> > You mean change L to D?
> >
> > If so, then you can edit the coordinates: pick one coordinate (say, x)
> > and multiply all the values by -1. That will give you a mirror image.
> > Do this in a pdb file or a restart file, etc. Of course, that will
> > disrupt its relationship to other residues, so you might need to do
> > other stuff.
> >
> >
> > On Mon, Feb 20, 2017 at 2:42 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> > > AFAIN, there's not.
> > >
> > > Hai
> > >
> > > On Mon, Feb 20, 2017 at 10:14 AM, Thomas Pochapsky <
> > pochapsk.brandeis.edu>
> > > wrote:
> > >
> > >> Is there a straighforward way to change the chirality of specific
> amino
> > >> acid residues using parmed?
> > >>
> > >> Thanks,
> > >> Tom Pochapsky
> > >>
> > >>
> > >>
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> >
> >
> > --
> > :-) Lachele
> > Lachele Foley
> > CCRC/UGA
> > Athens, GA USA
> >
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Received on Tue Feb 21 2017 - 14:00:04 PST
