On Tue, Nov 01, 2011, James Starlight wrote:
>
> E.g for this exersice I'd like to build CAP groups on N and C termii of
> each chain of my protein.
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.
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
>
> 2- What xleap force field should I use for such parametrisation? My protein
> consist of some non-standart amino-acids ( D- isomers) like D-leucyn and
> D-valine. What leap force field already has parametrisation for such
> aminoacids?
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.
> Also I want to perform further simulation ig Gromacs for instance so I'm
> looking for a force field wich could be best compatible with some gromacs
> force fields like gromos etc
You'd have to check, but my guess is the same thing is true for gromacs: the
force field for D-alanine is the same as for L-alanine. (Please note that
this is a guess...I've never used gromacs myself.)
....dac
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Received on Tue Nov 01 2011 - 08:00:03 PDT
