[gmx-users] Unneccessary bonding

[Justin A. Lemkul]

abdullah ahmed wrote:
> Dear Mr. Periole,
> 
> The atoms that are getting close are oxygen from a GLU residue and 
> hydrogen from a LYS residue.

I don't see anything wrong with a 1.4-A distance between these atoms.  Why do 
you suspect a problem (besides the non-existent bond)?

-Justin

> 
> 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 <mailto:x.periole at rug.nl>
>     To: gmx-users at gromacs.org <mailto: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 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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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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