Re: [AMBER] Residue chirality

From: <>
Date: Tue, 9 Jul 2013 08:25:54 -0700


Thank you everyone for your suggestions. I think Dr. Simmerling's idea of
using SwissPDB to add missing atoms into a PDB containing only the
backbone is easy to do. My peptide is large so it's tedious to invert the
chiral centers manually using "transform".

Previously when I did mutations, I deleted everything except C, O, N, CA;
and that might cause the problem. I should have kept also HA and CB from
the old residue template (assuming the old template has correct
chirality). I haven't tried but I think it should work. However, if there
is an atom clash, can minimization lead to inverted chiral center?

Thank you,


> On Tue, Jul 9, 2013 at 8:53 AM, Carlos Simmerling <
>> wrote:
>> Is the goal here the other chirality, or is that the problem?
> I think they were trying to work around the problem of tleap adding in the
> sidechain with the wrong chirality by building with a residue template
> that
> itself had the wrong chirality (the "two wrongs make a right" idea).
> I may have gotten it wrong, but I was just trying to suggest an easier way
> of creating a residue with an inverted chirality directly in tleap rather
> than going through the trouble of an external program and having to do all
> of the work of atom naming and charging.
> All the best,
> Jason
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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> AMBER mailing list

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Received on Tue Jul 09 2013 - 08:30:03 PDT
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