[gmx-users] electro-static interaction not made

[XAvier Periole]

On May 11, 2010, at 11:37 AM, abdullah ahmed wrote:

> Dear GROMACS users,
>
> I have a protein structure with two oppositely charged residues  
> facing each other. They are close enough for an electrostatic  
> interaction to occur between them. However, this does not occur.  
> After minimization they are in the exact same positions as before.
So you have a new problem? Now you do not have the interaction  
anymore!?!??!
Last week you had it too close and wanted to avoid your residues to  
come that close!

Last week you also had several persons giving you advices about this  
issue and
everyone I believe agreed that this was certainly not the way to  
proceed to show
the effect or potential effect of a mutation.
More than a meaningless minimization a graphic illustration of the  
salt-bridge broken
by the mutation would probably be a better argument.

If you want a meaningful number you'll have to go for more  
sophisticated methods.

Note that the difference you see is 1000 kJ/mol, this is not small!

XAvier.
>
> Is there some way to confirm that an electrostatic interaction is  
> not being made in the structure with two charged residues facing  
> each other? And if this is the case, do you have any idea as to why  
> this is happening?
>
> Perhaps the following information will prove helpful:
>
> I have another structure where there is only one charge (GLU) and  
> one uncharged residue in the same positions as the charged residues  
> in the previous structure. The coulomb energy values of the two  
> structures after minimization do not show much difference (-3.9e+04  
> compared to -4.0e+4, where -4.0e+04 corresponds to the structure  
> with two charges facing each other). Theoretically, this difference  
> should be greater as the unsatisfied single charge is not as stable.  
> To me the similar coloumb energies suggest that the electrostaic  
> interactions are not being made in the structure with two opposite  
> charges.
>
> My .mdp file is as follows:
>       ;
>       ;    User spoel (236)
>       ;    Wed Nov  3 17:12:44 1993
>       ;    Input file
>       ;
>       cpp                 =  /usr/bin/cpp
>       define              =  -DFLEXIBLE
>       constraints         =  none
>       integrator          =  steep
>       nsteps              =  1000
>      ;
>      ;    Energy minimizing stuff
>      ;
>      emtol               =  2000
>      emstep              =  0.01
>
>     nstcomm             =  1
>     ns_type             =  grid
>     rlist               =  1
>     rcoulomb            =  1.0
>     rvdw                =  1.0
>     Tcoupl              =  no
>     Pcoupl              =  no
>     gen_vel             =  no
>
>
> Thank you in advance!
> Abdullah
>
>
>
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