yes, absolutely CB not CA!
On Tue, Feb 21, 2017 at 4:39 PM, Osman, Roman <roman.osman.mssm.edu> wrote:
> Carlos,
>
> You probably meant CB not CA!
>
> Rami
>
> On Feb 21, 2017, at 4:33 PM, Carlos Simmerling <
> carlos.simmerling.gmail.com<mailto: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).
>
> On Tue, Feb 21, 2017 at 4:26 PM, Lachele Foley <lf.list.gmail.com<mailto:
> 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<mailto:nhai
> .qn.gmail.com>> wrote:
> AFAIN, there's not.
>
> Hai
>
> On Mon, Feb 20, 2017 at 10:14 AM, Thomas Pochapsky <
> pochapsk.brandeis.edu<mailto: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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> Roman Osman
> Professor of Structural and Chemical Biology
> Mount Sinai School of Medicine
> New York, NY 10029
> (212) 659-8627
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Received on Tue Feb 21 2017 - 14:00:05 PST
