Dear Mr. Periole,

The atoms that are getting close are oxygen from a GLU residue and hydrogen 
from a LYS residue. 

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
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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