On Tue, Nov 01, 2011, James Starlight wrote:
>
>
> > Capping groups in Amber are called ACE (acetyl), NME (N-methyl) and NH2
> > (NH_2). They are treated as regular amino acids, e.g. your sequence might
> > be ACE-ALA-ALA-ALA-NME, for a tri-alanine helix with capping groups.
> >
> > So If my initial structure consist of only amino acids atoms could I build
> CAPS via xleap or coordinates for this caps already must be in the initial
> structure?
You can use xleap, although it's a bit clunky as an interactive editor.
> >
> > So the problem is simple :) I havenot found how to save output in pdb :)
See the "savePdb" command in LEaP.
> So I needn't create addition functional groups for D isomers? Have they
> already included in the param for instance leaprc.ff10?
Yes. But I really encourage you to think about this carefully, and to
understand why there is no force-field difference between D and L-amino
acids. For example, try computing the energy of a L-amino acid, then the
energy of its mirror image. Make this be something that you are confident
you understand, not something you took my word for.
...dac
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Received on Tue Nov 01 2011 - 09:00:04 PDT
