[gmx-users] Unneccessary bonding

XAvier Periole x.periole at rug.nl
Mon May 3 18:37:43 CEST 2010 

On May 3, 2010, at 6:27 PM, 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)
genbox is not necessarily able to place water molecules in small  
confined spaces
in a protein. You should check the pdb structure and see if there is  
not a water molecule
in that "space". Note that this was only a idea ... not necessarily  
your problem.
a better probe of the distance between the two residue side chain  
would be to use
the C of the COO group and the N of the NH3 group. You might observe  
reorientation
the the "satellite atoms" (O and H) while the center of the group is  
actually keeping
a reasonable distance.
Basically all goes in checking what kind of deformation you observe  
during your
minimization, a single distance is not necessarily meaningful.
> If you like I can send you the structures in PDB form.
Not necessary
>
> > 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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