AMBER Archive (2009)

Subject: Re: [AMBER] Do I need to modify the cap residues

From: nicholus bhattacharjee (nicholusbhattacharjee_at_gmail.com)
Date: Mon Apr 06 2009 - 23:51:22 CDT

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_at_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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