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.
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
_________________________________________________________________
Hotmail: Powerful Free email with security by Microsoft.
https://signup.live.com/signup.aspx?id=60969--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
