Re: AMBER: Protonation of Aspartate

From: Adrian Roitberg <>
Date: Thu, 08 Feb 2007 12:17:11 -0500

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
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Received on Sun Feb 11 2007 - 06:07:23 PST
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