Re: Should you cap C and N termini?

From: Vlad Cojocaru (
Date: Thu Feb 18 2016 - 09:31:56 CST

We generally use caps because our systems are individual domains within
larger proteins ... But if you simulate entire proteins, charged termini
should be more appropriate.

Whether it makes a difference or not, I cannot say as we never tested
this issue in particular.


On 02/18/2016 02:09 PM, ashika torikora wrote:
> Hello all,
> My question is more of a broad, open-ended question. I would like to
> get some opinions on whether C and N terminal caps should be added to
> proteins in simulations.
> Thanks y'all,
> xoxo

Dr. Vlad Cojocaru
Computational Structural Biology Laboratory
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]

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