[gmx-users] Unneccessary bonding

Justin A. Lemkul jalemkul at vt.edu
Mon May 3 18:30:18 CEST 2010 


abdullah ahmed wrote:
> 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.
> 

If the two residues are in the protein interior, there likely won't be water 
there (nor should there be).  Electrostatic interactions in the core of a 
protein is an interesting topic and there is lots of literature about it, 
including whether or not certain ionization states should exist and whether or 
not they are functionally relevant.

For charged residues in a protein interior, I see no problem whatsoever with 
what you're seeing.

-Justin

>  > 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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-- 
========================================

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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