On May 3, 2010, at 6:12 PM, Justin A. Lemkul wrote:



abdullah ahmed wrote:
Dear Mr. Periole,
The atoms that are getting close are oxygen from a GLU residue and hydrogen from a LYS residue.

I don't see anything wrong with a 1.4-A distance between these atoms. Why do you suspect a problem (besides the non-existent bond)?
Agreed! This is fine ... the question is why they go from 3.5 to 1.4 ... are they
embedded in the protein interior? At the surface of the protein ....
may be a missing water molecule in between them?

-Justin

Abdullah
------------------------------------------------------------------------
From: x.peri...@rug.nl
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Unneccessary bonding
Date: Mon, 3 May 2010 18:00:43 +0200
On May 3, 2010, at 5:52 PM, abdullah ahmed wrote:
Thank you very much for your reply, I agree it is probably a visualization of the effect, and that there
   is no bond. However, the distance between the two atoms
   participating in this "phantom bond" is 1.4 A°. Isn't that too
close? Shouldn't it be considered a clash? 1.4 is short for sure! an H-bond goes down to 1.0 ... and charged ions make (depending on their size) bonds with water oxygen around 2.0 ... If you have two opposite charges in front of each other that might well be happening! What kind of atoms are the ones getting close? Abdullah ------------------------------------------------------------------------
   From: x.peri...@rug.nl <mailto:x.peri...@rug.nl>
   To: gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>
   Subject: Re: [gmx-users] Unneccessary bonding
   Date: Mon, 3 May 2010 17:36:29 +0200
   On May 3, 2010, at 5:16 PM, abdullah ahmed wrote:
Hello, I am a new user to GROMACS and so this question maybe somewhat naive. My objective is to run a few steps of minimization on a PDB
       structure and then obtain the energy value. To do so I ran the
procedure suggested in the tutorial called "speptide" using the .mdp file provided in this procedure. The structure I am using has two oppositely charged residues
       facing each other. The initial distance(3.2 A°) is such that
ionic interactions should occur between them, thereby creating a
       low coloumb energy score after minimization/molecular dynamics
(check by looking at the log-file). However, a covalent bond is being created between them instead. This should not be happening. What do you mean a covalent bond is being created! This is basically not possible! Would that just be a visualization effect? This could result from
   the fact that the two atoms
   get really close to each other and thereby your visualization
   program thinks it is a covalent
   bond.
       Does anyone have any ideas on what may be happening and how I
can fix it? If this information is not sufficient, please let me know, and
       thank you in advance.
Abdullah Ahmed ------------------------------------------------------------------------
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--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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