Dear David,
You still din't tell me how to add caped residues in my
existing PDB. I have tried in the following way but am not sure if it is the
right way.
> mol = loadpdb my.pdb
>mol = sequence {ACE mol NME}
Please let me know if it is the right way to add caped residues. If it is
not then how do I add. Thanx in advance.
On Mon, Apr 6, 2009 at 2:57 PM, David A. Case <case.biomaps.rutgers.edu>wrote:
> On Mon, Apr 06, 2009, nicholus bhattacharjee wrote:
>
> > I want to
> > know that if we don't cap the ends will it hamper the MD simulation.
>
> Whether to add cap residues (like ACE, NME) usually depends on what
> experiments you want to compare with. Biological proteins don't have
> cap residues, synthetic peptides often do. Your goal is to make the
> chemistry of what you are simulating as close as you can to the
> real-life situation you are interested in.
>
> ...dac
>
>
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--
Nicholus Bhattacharjee
PhD Scholar
Department of Chemistry
University of Delhi
Delhi-110007 (INDIA)
Phone: 9873098743(M)
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Received on Wed Apr 08 2009 - 01:14:39 PDT
