[gmx-users] Unneccessary bonding

[abdullah ahmed]

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.periole at rug.nl
To: gmx-users at 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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