Re: AMBER: problems in adding ACE and NME group

From: David A. Case <>
Date: Thu, 28 Jun 2007 09:04:52 -0700

On Thu, Jun 28, 2007, backy wrote:

> Sorry, I am a little confused about that. So do you mean that even for a
> protein with residue index( ex: 100-500), the capping process is no need as
> its energy was minimized? If so, for this kind of protein, what is the
> "common" charge assigned to the protein terminal?

It depends on what experiments you are trying to compare to. Actual proteins
in experiments would almost never have these capping groups. If there is
really something there that is not visible in the X-ray density, I think
most people would just simulate residues 100-500, with the end residues either
charged or uncharged. If it makes a difference which choice you make, then
you probably have an ill-defined simulation problem anyway.


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Jul 01 2007 - 06:07:22 PDT
Custom Search