[gmx-users] error while energy minimization with the protein fixed

[Justin A. Lemkul]

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

-- 
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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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