Hello everyone,
I have a question regarding the results of minimization. I have two structures
that are the same except for 2 residues in the core of the structure that have
been changed from luecine to to glycine. The leucine structure is very well
packed and the core is hydrophobic. The introduction of two glycines in the
center creates a a cavity in this hydrophobic region.
I had expected the leucine structure to have better(lower) energy after
optimization, however, the opposite was true. I have run minimization in vacuum
and with water (water enters the cavity) and the structure with glycine has
better energy in both cases.
The minimization procedure is what I think is standard, the em file is as
follows:
;
; User spoel (236)
; Wed Nov 3 17:12:44 1993
; Input file
;
cpp = /usr/bin/cpp
define = -DPOSRES
constraints = none
integrator = steep
nsteps = 1000
;
; Energy minimizing stuff
;
emtol = 20
emstep = 0.01
nstcomm = 1
ns_type = grid
rlist = 1
rcoulomb = 1
rvdw = 1
Tcoupl = no
Pcoupl = no
gen_vel = no
I am using gromacs on windows through cygwin.
Thank you in advance for your help,
Abdullah
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