On Thu, Oct 11, 2012 at 2:36 PM, Changqing Yan <ycqchemical.gmail.com>wrote:
> Dear all,
>
> As you know the usual amino acid created in Amber is left-handed. So anyone
> knows how to create a right-handed amino acid in leap? For example, I want
> to create a right-handed phe amino acid in a peptide sequence SVRPfVDRE.
> What should I do?
>
The templates are right-handed. If your starting PDB has a right-handed
PHE amino acid, then it will not switch the chirality to left-handed.
If, on the other hand, you want to use the templates in tleap and include a
right-handed helix, I have a way. You need to create a new residue as a
copy of PHE and then 'reflect' it through a mirror plane (that inverts
chirality).
For instance:
dPHE = copy PHE
transform dPHE { {1 0 0} {0 1 0} {0 0 -1} }
And then use "dPHE" in place of PHE in your "sequence" command.
HTH,
Jason
P.S. -- Make sure you visualize the result to make sure you have what you
want.
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Oct 11 2012 - 07:30:05 PDT
