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
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 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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