Re: AMBER: general questions

From: <>
Date: Tue, 07 Sep 2004 13:11:01 +0200

Dear Marsita,
Amber protonates the residues according to its
templeates, so you have to chose the protonation
site and tell the program specifying the correct
residue name (HID, HIE or HIP for example). In
order to know or guess the protonation state you
need some prior information, deriving for example
from a nuclear magnetic resonance experiment or
from the knowledge of the situation you are trying
to simulate. For example, histidine in the
cathalitic triad of some protease may be doubly
protoneted at some step of the reaction, this is
HIP , positive histidine. Even the knowledge of
the pH of the solution may help (at rather acidic
pH histidine is doubly protonated, HIP, positively
charged histidine). If there is no prior
information, the program has a default HID
protonation, which is the most usual.
For the second question, amber needs a neutral
sistem in order to handle long range
(electrostatic) interactions in the periodic box
representation. If you use periodic conditions, no
matter if solvent is present, the PME algoritm
needs a neutral sistem, and the program
neutralises by itself the charge residues that mey
be present. If this residues are not small
residues due to the computatin of all the charges
in the molecule, that mey be non exacly 0 for
precision reasons, but are "true" charges, the
effect of forcing neutrality (sort of automatig
placing of a diffuse charge plasma through the
sistem) may be serious. Amber, as you know, allows
you to neutralize the sistem by adding a proper
number of counterions in starting positions
selected using a grid of electrostatic potential.
This device is in the leap program.
hoping this can be of some help
              Stefano Pieraccini
----- Original Message -----
From: Marsita M <>
Date: Monday, September 6, 2004 5:58 pm
Subject: AMBER: general questions
> dear list,
> i have a few general questions about amber, and
i hope someone can
> help me
> answering this question
> 1) How to know the correct protonation state for
histidines before
> we create
> the prmtop file? does it require knowledge in
chemistry? (which i'm
> absolutely lacking since my background is not
chemistry) .. what
> would
> happen, if we misinterpret the correct histidine
protonation site?
> such as
> HIE instead of HID etc.
> 2) since i'm new to amber and my chemistry is
very bad, i have one
> silly
> question to ask, is it appropriate to neutralize
the system if the
> simulation is to be run in vacuo? or it wouldnt
make any difference
> at all
> since it's in vacuo where it would have been if
it were to run in
> water?
> thank you in advance
> Undgå pop-ups med MSN Toolbar - hent den
> gratis!
> ---
> The AMBER Mail Reflector
> To post, send mail to
> To unsubscribe, send "unsubscribe amber" to

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Fri Sep 10 2004 - 13:25:59 PDT
Custom Search