prakash verma wrote:
Dear All,
while energy minimization with the protein fixed i am getting following
error:
*t = 0.011 ps: Water molecule starting at atom 21089 can not be settled.
Check for bad contacts and/or reduce the timestep.*
Even if i am reducing timesteps its not working.
The minim.mdp file which i have used is:;
ntegrator = steep ; Algorithm (steep = steepest descent
minimization)
emtol = 1000 ; Stop minimization when the maximum
force < 1000.0 kJ/mol/nm
dt = 0.01
emstep = 0.01 ; Energy step size
nsteps = 20000 ; Maximum number of (minimization) steps
to perform
constraints = all-bonds ; convert all bond to constraints
; Parameters describing how to find the neighbors of each atom and how
to calculate the interactions
nstlist = 5 ; Frequency to update the neighbor list
and long range forces
ns_type = grid ; Method to determine neighbor list
(simple, grid)
rlist = 1 ; Cut-off for making neighbor list
(short range forces)
coulombtype = PME ; Treatment of long range electrostatic
interactions
rcoulomb = 1 ; Short-range electrostatic cut-off
rvdw = 1 ; Short-range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions (yes/no)
optimize_fft = yes
pme_order = 4
fourierspacing = 0.15
; Non-equilibrium MD stuff
freezegrps = Protein Sol
freezedim = Y Y Y N N N
By freezing the protein, you are probably preventing a bad contact (or more than
just one) from being resolved. Any particular reason you're freezing the
protein during EM? Seems self-defeating to me.
Open the structure in your favorite visualization program, see where the
problematic water molecule is, and try to identify what it is clashing with.
-Justin
--
========================================
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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