AMBER Archive (2009)

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

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Mon Apr 06 2009 - 13:57:02 CDT

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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