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?
Abdullah
From: x.peri...@rug.nl
To: 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 atomsget really close to each other and thereby your
visualization program thinks it is a covalentbond.
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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