David,
> 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?
> In the end, you need to get some starting coordinates for both the regular
> amino acids and the capping groups. Where these come from is very highly
> dependent on the problem
>
> So the problem is simple :) I havenot found how to save output in pdb :)
In tutorial I found only possible way to save the topology files
> Amber force fields can (and have) been used for both L- and D-amino acids:
> the
> difference is only in the coordinates, not in the force fields.
>
So I needn't create addition functional groups for D isomers? Have they
already included in the param for instance leaprc.ff10?
James
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Received on Tue Nov 01 2011 - 08:00:07 PDT
