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)?
-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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