swagata chakraborty wrote:
Hi,
Thanks a lot for the reply and the suggestion.
I am carrying the simulation in 100% DMSO( no water) at 318 K.the em.mdp
file is as follows:
define = -DFLEXIBLE
constraints = none
integrator = steep
dt = 0.002 ; time step
nsteps = 1000 ; number of steps
nstlist = 10 ; update pairlist
ns_type = grid
coulombtype = PME
rcoulomb = 1.0
vdwtype = cut-off ;shift
rlist = 1.0 ; cut-off for ns
rvdw = 1.4
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
;
; Energy minimizing stuff
;
emtol = 1000
emstep = 0.01
DSSP is giving change in the sheet, loop and turn content although the
helix content remains the same on comparison with the native pdb. What
is more surprising is that though it is a homodimer the structure change
in the two monomers is not the same ( in one monomer the sheet is
extended while in the other it is not.
Is it fine if I try to first energy minimize the structure in vacuum and
then solvate in DMSO box and run the MD without minimizing in DMSO
That sounds like bad protocol. You should do an energy minimization of the
complete system, even if you don't like the results. Incorrect output is
indicative of something fundamentally wrong, perhaps within the force field itself.
box. Also when I am trying any other force field an error is coming
'Atomtype SD not found'.
Force field files can't be mixed haphazardly. Parameters are typically derived
and distributed for one force field at a time.
For check I ran the MD of my protein in water using G43a1 forcefield,
in that also after em step the loop is turning into a beta sheet.
As I recall, your original message said the problem initially appeared with
53A6. Comparing the results with 43A1 is not a very good test. I know 53A6 is
prone to giving extended configurations (per the literature), so likely 43A1 has
some similarities, since bonded parameters are very similar. A better test
would be any one (or all) of OPLS-AA, AMBER, or CHARMM. Of course, this
requires proper DMSO parameters for these force fields, but no one ever said
life was easy :)
Please let me know if there is any manual on DMSO box generation and
equilibration.
There aren't how-to's for everything imaginable, but there is relevant
literature. A quick search will turn up the 53A6 DMSO parameters, which should
be a reasonable starting point for whatever you want to learn.
-Justin
Regards,
Swagata Chakraborty
Research Scholar,
Department of Chemical Sciences,
Tata Institute of Fundamental Research,
Mumbai-400005
Swagata Chakraborty
Research Scholar,
Department of Chemical Sciences,
Tata Institute of Fundamental Research,
Mumbai-400005
--
========================================
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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