bound ion

Miri Hirshberg m-hirshb at ANIKA.NIMR.MRC.AC.UK
Mon Nov 17 17:40:32 EST 1997


>I am refining a structure that has an ion (probably Sodium) bound to the
>protein with octahedral coordination.  The ion interacts with two
>protein atoms and four waters.  What is the correct way to input this
>information into X-PLOR?  I suspect it requires use of a patch but I
>cannot figure out how to do it from the examples in the version 3.1
>manual or any of the examples I've found online.
>
>
>-- 
>Robert Grant, Ph.D.
>Department of Biological Chemistry and Molecular Pharmacology
>Harvard Medical School
>Boston, MA
>email: grant at ganesh.med.harvard.edu

Dear Robert,

 you can keep the sodium ion in place using NOE's

 In you .inp file have something like

 -------------------
 noe  reset
  nres=100
  class all @cal.noe
  potential all square
  scale all 50.
  ?
 end
---------------------

while the cal.noe looks like

-------------
set echo=false end
set wrnlev=0 end

ASSIGN (RESID   20 AND NAME OD2  ) (RESID   149 AND NAME CAL  )  2.4 0.2 0.7
ASSIGN (RESID   22 AND NAME OD2  ) (RESID   149 AND NAME CAL  )  2.2 0.4 0.5
ASSIGN (RESID   24 AND NAME OD1  ) (RESID   149 AND NAME CAL  )  2.3 0.3 0.6
ASSIGN (RESID   26 AND NAME O    ) (RESID   149 AND NAME CAL  )  1.9 0.7 0.2
ASSIGN (RESID   31 AND NAME OE1  ) (RESID   149 AND NAME CAL  )  2.3 0.3 0.6
							                    

set echo = true end
set wrnlev = 5 end

-------------

Miri


===========================================================================
Miriam Hirshberg                           Tel: (+44)0181-959-3666 ext 2520
National Institute for Medical Research    
Protein Structure                          Fax: (+44)0181-906-4477
The Ridgeway                               email: m-hirshb at anika.nimr.mrc.ac.uk
Mill Hill, London NW7 1AA   UK                  (192.107.168.100)
===========================================================================






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