[AMBER] Metal site hybrid bonded model

From: Lizelle Lubbe <LBBLIZ002.myuct.ac.za>
Date: Fri, 13 Oct 2017 12:45:30 +0000

Hi Pengfei and AMBER users,

Following some trouble with applying the bonded model for the zinc site in my protein, Pengfei Li advised me to try a hybrid bonded/non-bonded model. The 2 coordinated histidines and glutamate residue are treated with the bonded approach while the zn-coordinated water molecule is treated with the non-bonded. The parameters used have been previously validated and published.

>From minimization through to equilibration everything looks fine when viewing the metal site. At the first few steps of production, however, the coordinated water molecule treated with harmonic restraint moves ~30 angstroms away from the zinc and its hydrogens are very stretched.

I think that perhaps this could be the result of having r4=100.0 in my RST file. Or is it caused by something else?
Would setting r4 equal to the wanted distance of r2=r3 prevent the water from moving away?
Or should I set it to perhaps something like r4=4.0 so that I still have a well for the distance restraint?

Here are my input files for production:

First Dynamic Simulation with Constant Pressure

 # Control section
  imin = 0,
  irest = 1,
  ntx = 5,
  ntb = 2, ntp = 1, pres0 = 1.0, taup = 1.0,
  cut = 10.0,
  ntc = 2, ntf = 2,
  temp0 = 300.0,
  ntt = 3, gamma_ln = 2, ig = -1,
  nstlim = 500000, dt = 0.002,
  ntwx = 5000, ntpr = 5000, ntwe = 5000, ntwr = -100000,
  ioutfm = 1,
  iwrap = 1,
  ntr = 0,
  ntwprt = 12497,
  nmropt = 1,
  &wt type = 'END'/

# Harmonic restraints for the restrained nonbonded model of ACE NDOM
&rst iat=12528,12493, r1=0., r2=2.056, r3=2.056, r4=100., rk2=66.54, rk3=66.54,/

Could someone also please explain to me what the following from prod_error means and if I can ignore it:
Note: The following floating-point exceptions are signalling: IEEE_DIVIDE_BY_ZERO

Kind regards

Lizelle Lubbe

PhD (Chemical Biology) candidate
Department of Integrative Biomedical Sciences
University of Cape Town
South Africa
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Received on Fri Oct 13 2017 - 06:00:13 PDT
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