On Thu, Aug 15, 2013, moitrayee.mbu.iisc.ernet.in wrote:
> I know that AMBER automatically assigns the Nterm and Cterm residues as
> NXXX and CXXX.
This substitution is defined in the leaprc file that you load. So there is
indeed a default behavior, but you can edit (a copy of) the leaprc file to
change the default behavior.
> My question is in that whether in an MD, the charges on an uncapped
> Nterm or Cterm can interact with the protein and bring about unusual
> distortions in the structure ? In other words, is it always necessary to
> cap the ends by say NME and ACE or AMBER does take care of this issue
> internally ?
Generally, proteins in the cell are uncapped, (which is why Amber has the
default that is does). Charges on the terminal residue certainly interact
with the rest of the protein (just as charges on charged side chains do).
Such interactions are a reasonably faithful model of physical reality (at
neutral pH where the C- and N-termini are charged); so I would not use the
term "unusal distortions" to describe their effects.
Capping groups are mostly used for synthetic polypeptides, where these groups
are actually present in the molecules being considered.
...dac
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Received on Thu Aug 15 2013 - 06:30:02 PDT
