amber tutorials/
crown tutorial

Crown Ether Setup Using Leap

The leaprc in this directory only loads the minimal things needed: the ions and water libraries, and the force field parameters. The AMBERHOME environment variable (or LEAPROOT in versions 5 or earlier) must be set to enable the ions and water libraries to be loaded.

Various intermediate and final stages are saved in the leap-format file, crown.lib.

Parameters

The ion vdw parameters in the standard force field file were derived to model interactions with waters defined as single, oxygen-centered spheres enclosing the hydrogens. Since the main focus of interest is the interaction between ion and crown ether, we override the ion vdw parameters with ones derived for interactions with guanosine carbonyl oxygens [frcmod.dat], in order to better approximate a solute-ion interaction. Since the vdw parameters used for the guanosine oxygen differ from the ones used for the crown oxygen, one could consider deriving new ion parameters for use with this oxygen (see table below).

Since the ions also are simultaneously in contact with waters, it is in fact impossible to model all contributions to ion binding optimally with the current method without allowing separate specification of solute-solute and solute-water vdw parameters.

Parameters for simulations with atomic polarizabilities are in a much more tentative state of development. Bond, angle and torsion parameters are the same; only nonbonded parameters are modified. Charges are scaled back by .8 (easily done using scaleCharges), and as of 1998, the water vdw is slightly modified to get correct water density. The polarizabilities for non-ions used here are from Applequist,JB; Carl,JR; Fung,K-K; JACS, 1972, vol 94(9), 2952-2960. The ion polarizabilities of 0.0 are based on results of Caldwell (0.0 can be used for first and second column elements of the periodic table).



             Various Oxygen VDW Parameters

                                                       R*       epsilon

    Guanosine carbonyl (Weiner et al. type 'O')        1.6        0.20
    Crown oxygen (Cornell et al. type 'OS')            1.6837     0.17

    TIP3P (type 'OW')                                  1.7683     0.152
    TIP3P (type 'OW') - polar                          1.779      0.1554

Setup

  Build residue template
	(if this was done in a previous session, 
		> loadoff crown.lib
	to reload)

  Load pdb of whole molecule:

	> crown = loadpdb cr6.pdb
	> edit crown

  Close the open bond:

     


  Hold down the two right buttons and push forward/back to zoom in/out.
  The middle button alone rotates, the right button translates, and
  the spacebar recenters the molecule.

	  - select 'Draw' mode and connect the carbons

  Save the crown molecule for future use (so bond doesn't need to be
  redrawn), and make toplogy/coordinate files for normal mode analysis:

	> saveoff crown crown.lib
	> saveamberparm crown crown_plain.top crown_plain.crd
	> saveamberparmpol crown crown_pol.top crown_pol.crd


  Make a new copy of the molecule and add complexed ion:

	> crownI = copy crown
	> edit crownI

	  - Unit / Import / Na+
	  - select 'Select' mode, select the ion, and 
	  - select 'Move' mode and move the ion to the center of the ring
		(use middle button to rotate everything)

	         

          - make sure ion is centered in the side view
		(again use middle button to rotate everything)

	         


  Add perturbation to ion:

	  - ion is still selected, so 'Edit / Edit selected atoms'
	  - fill in the 'PERTURB/PERT' parameters as shown

     


  Save system in leap format for future reference and
  save 'parm' files for dynamics & perturbation:

	> saveoff crownI crown.lib
	> saveamberparm crownI crown_na.top crown_na.crd
	> saveamberparmpert crownI crown_na_k.top crown_na_k.crd


  Make versions with scaled charges for simulations with atomic
  polarizabilities and save 'parm' files:

	> crownpol = copy crown
	> scalecharges crownpol .8
	> saveamberparm crownpol crown_pol.top crown_pol.crd
	> crownIpol = copy crownI
	> scalecharges crownIpol .8
	> saveamberparm crownIpol crown_na_pol.top crown_na_pol.crd
	> saveamberparmpert crownIpol crown_na_k_pol.top crown_na_k_pol.crd

  (The scaled-charge model is not saved to crown.lib, since
  it can be easily reproduced as above using scalecharges.)

  
  Follow the same steps to build a K+ complex with perturbation from
  K+ -> Cs+:

	> crown2 = copy crown
	> edit crown2

  [import K+, place the ion, edit selected atoms,
  and make the perturbed atom type Cs.]

	> saveoff crown2 crown.lib
	> saveamberparm crown2 crown_k.top crown_k.crd
	> saveamberparmpert crown2 crown_k_cs.top crown_k_cs.crd

Demo by Bill Ross, April 1998.