[gmx-users] Unneccessary bonding

[abdullah ahmed]

Dear Mr. Periole,

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

Abdullah

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