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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