protein with selenomethionine

Ethan A Merritt merritt at u.washington.edu
Wed Aug 12 18:09:34 EST 1998


In article <Pine.GSO.3.96.980812175048.7987A-100000 at mail1.sas.upenn.edu>,
Yi Mo <yimo at sas.upenn.edu> wrote:
>We are refining a protein structure with selenomethionines. Could someone
>kindly provide us a parameter and topology patch for the Selenomethionine
>residue? Thanks a lot.

The following files define a new residue type SME, with all atom
types the same as in the standard files parhcsdx.pro and tophcsdx.pro
other than the selenium itself.

				Ethan A Merritt
				merritt at u.washington.edu


semet.par
=========
Remarks Parameters for Se in selenomethionine
Remarks values taken from Kleywegt autogenerated SeMet 
Remarks Ethan A Merritt - 5 Aug 1998

 set echo=false end

 BOND CH3E SE     1000.0  2.063 
 BOND SE   CH2E   1000.0  1.782 

 ANGLe CH2E CH2E SE      500.0   102.78 
 ANGLe CH2E SE   CH3E    500.0    97.28 

 DIHEdral CH1E CH2E CH2E SE      750.0 0   180.00 
 DIHEdral CH2E CH2E SE   CH3E    750.0 0   -90.00 

 NONBonded SE   .0430 3.510       .0430   3.510  ! assuming Selenium

 set echo=true end


semet.top
=========
Remarks Modify MET residue from tophcsdx.pro to be
Remarks SME Seleno-methionine instead
Remarks Ethan A Merritt - 5 Aug 1998

 set echo=false end

 MASS SE   78.96000 

!------------------------------------------------------------------

RESIdue SME
 GROUp
  ATOM N    TYPE=NH1   CHARge=-0.35   END
  ATOM H    TYPE=H     CHARge= 0.25   END
  ATOM CA   TYPE=CH1E  CHARge= 0.10   END
  ATOM CB   TYPE=CH2E  CHARge= 0.00   END
  ATOM CG   TYPE=CH2E  CHARge= 0.06   END
  ATOM SED  TYPE=SE    CHARge=-0.12   END
  ATOM CE   TYPE=CH3E  CHARge= 0.06   END
  ATOM C    TYPE=C     CHARge= 0.55   END  !#
  ATOM O    TYPE=O     CHARge=-0.55   END  !#

 BOND N    CA
 BOND CA   C
 BOND C    O
 BOND N    H
 BOND CA   CB
 BOND CB   CG
 BOND CG   SED
 BOND SED  CE

 DIHEdral N    CA   CB   CG
 DIHEdral CA   CB   CG   SED
 DIHEdral CB   CG   SED  CE

 IMPRoper CA   N    C    CB  !tetrahedral CA

 DONOr H    N
 ACCEptor O C

END {SME}




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