AMBER Archive (2007)

Subject: Re: AMBER: Protonation of Aspartate

From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
Date: Thu Feb 08 2007 - 11:17:11 CST

sai vikram wrote:
> i want to protonate the inner oxygen(OD1) of aspartate.
> can anybody tell me?
> i know about ASH( amber atom type for protonated aspartate) but that
> protonate the outer oxygen(OD2) plz reply soon
>
> thanks in advance
>
well, this is a question that I will try very hard to answer nicely.
What is the difference between an inner and outer H ?
OD1 and OD2 are JUST names !

you can switch those names in your pdb and then you get a proton in the
right place, you can wait until the dynamics flips them, or many other ways.
Basically, there is NO difference between them except the name !

There IS a difference between syn and anti protonation but that is an
issue of the coordinates and not the residue definition. 

-- 
                            Dr. Adrian E. Roitberg
                              Associate Professor
               Quantum Theory Project and Department of Chemistry

University of Florida                         PHONE 352 392-6972
P.O. Box 118435                               FAX   352 392-8722
Gainesville, FL 32611-8435                    Email adrian_at_qtp.ufl.edu
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