I've done this in tleap many times and it does work. The issue here is
probably in the details. What was the old a new sidechain? What is nearby?
When leap built it, did it fit without clash? Was the chivalry wrong coming
from leap, or after some minimization?
Note that leap can do this, but it won't try to optimize the location. In
most cases you probably want to use a different program to build initial
structures, not leap. Swisspdb does a reasonable job of sidechain
placement.
On Jul 9, 2013 5:25 AM, "Karl N. Kirschner" <kkirsch.scai.fraunhofer.de>
wrote:
> Hi,
>
> At one time there was a bug concerning this in tleap (and g/sleap??),
> and I am not sure if it was ever corrected. If I recall correctly, the only
> work-around I found was to construct the enantiomer using an external
> editor (e.g. PyMol) and load it into xleap. This preserved the connectivity
> and dihedral angles.
>
> Cheers,
> Karl
>
> ----- Original Message -----
> From: tdo.chem.ucsb.edu
> To: amber.ambermd.org
> Sent: Tuesday, July 9, 2013 11:07:58 AM
> Subject: [AMBER] Residue chirality
>
> Hello,
>
> I try to perform mutations on a peptide by removing the sidechain atoms
> and replacing the old residue names with new residue names, then letting
> tleap add in the missing atoms. I check the chirality of the residues and
> find out that I don't have the correct chirality (i.e., I compute the
> chirality dihedral angles and obtain both positive and negative numbers).
>
> Is there any better way to do mutations with Amber/tleap? How can I fix
> the incorrect chirality?
>
> Thank you,
>
>
>
>
>
>
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Received on Tue Jul 09 2013 - 05:30:03 PDT
