remark   file top_zinc.pro  version 0.3  date 10-Apr-97
remark   topology for zinc finger
remark   Author: Jurgen F. Doreleijers, RUU
remark   version 0.2 added a different topology patch CYS2        date  9-Apr-97
remark   version 0.3 added angles for patch CYS2                  date 10-Apr-97
remark   version 0.4 added a different topology patch ZINE        date 10-Apr-97
remark   version 1.0 deleted redundant angles and impr            date 15-May-97


SET ECHO=FALSE END

mass ZN 65.39

RESIdue zinc                           {*Generate the cluster itself.   *}
				       {*The name zinc has to match what*}
				       {*you are using for the residue  *}
GROUP                                  {*name in the coordinate file.   *}
   ATOM ZN1    type ZN  charge  1.0 end
END  {*JFD: to overcome the negative total charge of the 2 His and 2 Cys*}



                               {* Add a chirality restraint on the zinc *}
                               {*         2 (ND1)                       *}
                               {*         |                             *}
                               {* (NE2) 1>ZN<3 (SG)                     *}
                               {*         |                             *}
                               {*         4 (SG)                        *}
PREsidue CHIR
   improper 1NE2 2ND1 3SG 4SG
END

							    {* C1   C2 *}
							    {*  \  /   *}
							    {*   Zn5   *}
							    {*  /  \   *}
							    {* H3   H4 *}
PREsidue ZINF
		 
  ADD BOND 5ZN1  1SG                     {*These are the covalent bonds*}
  ADD BOND 5ZN1  2SG                     {*between the CYSs and the    *}
  ADD BOND 5ZN1  3NE2                    {*cluster.                    *} 
  ADD BOND 5ZN1  4NE2

  ADD ANGLe  1CB 1SG 5ZN1
  ADD ANGLe  2CB 2SG 5ZN1

  ADD ANGLe  3CE1 3NE2 5ZN1
  ADD ANGLe  3CD2 3NE2 5ZN1
  ADD ANGLe  4CE1 4NE2 5ZN1
  ADD ANGLe  4CD2 4NE2 5ZN1

  ADD ANGLe  1SG 5ZN1 2SG
  ADD ANGLe  1SG 5ZN1 3NE2
  ADD ANGLe  1SG 5ZN1 4NE2

  ADD ANGLe  2SG 5ZN1 3NE2
  ADD ANGLe  2SG 5ZN1 4NE2

  ADD ANGLe  3NE2 5ZN1 4NE2

  improper 3ND1 3CE1 3NE2 5ZN1         {* To keep Zn in plane with the His *}
  improper 3CG  3CD2 3NE2 5ZN1
  improper 4ND1 4CE1 4NE2 5ZN1         {* Chirality has to be done yet *}
  improper 4CG  4CD2 4NE2 5ZN1


END

 {* Only difference from ZINF is the coordination of H4 which is now   *}
 {*  by its ND1 in stead of its NE2                                    *}                          
                                                            {* C1   C2 *}
							    {*  \  /   *}
							    {*   Zn5   *}
							    {*  /  \   *}
							    {* H3   H4(ND1) *}
PREsidue ZINE
		 
  ADD BOND 5ZN1  1SG                     
  ADD BOND 5ZN1  2SG                     
  ADD BOND 5ZN1  3NE2                    
  ADD BOND 5ZN1  4ND1

  ADD ANGLe  1CB 1SG 5ZN1
  ADD ANGLe  2CB 2SG 5ZN1

  ADD ANGLe  3CE1 3NE2 5ZN1
!  ADD ANGLe  3CD2 3NE2 5ZN1 redundant
  ADD ANGLe  4CG  4ND1 5ZN1
!  ADD ANGLe  4CE1 4ND1 5ZN1 redundant

  ADD ANGLe  1SG 5ZN1 2SG
  ADD ANGLe  1SG 5ZN1 3NE2
  ADD ANGLe  1SG 5ZN1 4ND1

  ADD ANGLe  2SG 5ZN1 3NE2
  ADD ANGLe  2SG 5ZN1 4ND1

  ADD ANGLe  3NE2 5ZN1 4ND1

  improper 3ND1 3CE1 3NE2 5ZN1         {* To keep Zn in plane with the His *}
!  improper 3CG  3CD2 3NE2 5ZN1 redundant
  improper 4CD2 4CG  4ND1 5ZN1         {* Chirality has to be done yet *}
!  improper 4NE2 4CE1 4ND1 5ZN1 redundant


END
			    
							    {* C2   C1   C  *}
							    {*  \  / \  /   *}
							    {*   Zn4  Zn5   *}
							    {*  /  \ /  \   *}
							    {* H3   C6   H  *}

PREsidue CYS2
		 
  ADD BOND 1SG  4ZN1                    {*These are the covalent bonds*}
  ADD BOND 1SG  5ZN1
  ADD BOND 2SG  4ZN1              
  ADD BOND 3NE2 4ZN1  

  ADD ANGLe  1SG  4ZN1 2SG
  ADD ANGLe  1SG  4ZN1 3NE2
  ADD ANGLe  1SG  4ZN1 6SG

  ADD ANGLe  2SG  4ZN1 3NE2
  ADD ANGLe  2SG  4ZN1 6SG

  ADD ANGLe  3NE2 4ZN1 6SG

  improper 3ND1 3CE1 3NE2 4ZN1         {* To keep Zn in plane with the His *}
  improper 3CG  3CD2 3NE2 4ZN1

END

SET ECHO=TRUE END