[gmx-users] Unneccessary bonding

abdullah ahmed abdullah_renk_ahmed at hotmail.com
Mon May 3 18:27:56 CEST 2010 

They are on the inside of the structure. I don't think it is caused by a water molecule, because I ran editconf and genbox again and got the same result. (I have assumed that water molecules are added to the structure in a random fashion in areas not already occupied by other atoms)

If you like I can send you the structures in PDB form. 

> From: x.periole at rug.nl
> To: jalemkul at vt.edu; gmx-users at gromacs.org
> Subject: Re: [gmx-users] Unneccessary bonding
> Date: Mon, 3 May 2010 18:18:31 +0200
> CC: 
> 
> 
> On May 3, 2010, at 6:12 PM, Justin A. Lemkul wrote:
> 
> >
> >
> > 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)?
> Agreed! This is fine ... the question is why they go from 3.5 to  
> 1.4 ... are they
> embedded in the protein interior? At the surface of the protein ....
> may be a missing water molecule in between them?
> >
> > -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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