Loading ...
Sorry, an error occurred while loading the content.
 

Covalent Linkage between ND2 and C

Expand Messages
  • laxmicantan gurunathan
    Dear CNS users, I am having a problem in connecting the carbohydrate moeity NAG(N-acetyl glucosamine) with the Asn residue of my protein.I used the following
    Message 1 of 4 , May 3, 2004
      Dear CNS users,

      I am having a problem in connecting the carbohydrate
      moeity NAG(N-acetyl glucosamine) with the Asn residue
      of my protein.I used the following script in the
      generate.inp file but it did not give any covalent
      linkage between the NAG & Asn.

      The refinement programme pushes the sugar from the
      residue and yields non covalent distance between
      ND2(Asn) and C (NAG).

      =========================== carbohydrate links
      ===========================}

      {* Select pairs of residues that are linked *}
      {* First entry is the name of the patch residue. *}
      {* Second and third entries are the resid and segid
      for the atoms
      referenced by "-" in the patch. *}
      {* Fourth and fifth entries are the resid and segid
      for the atoms
      referenced by "+" in the patch *}
      {+ table: rows=6 numbered
      cols=6 "use" "patch name" "segid -" "resid
      -" "segid
      +" "resid +" +}

      {+ choice: true false +}
      {===>} carbo_use_1= true;
      {===>} carbo_patch_1="B1N";
      {===>} carbo_i_segid_1="A"; carbo_i_resid_1=95;
      {===>} carbo_j_segid_1="A"; carbo_j_resid_1=501;

      Here 95 refers to ASN and 501 refers to NAG.I have
      only one carbohydrate residue and i need to have a
      N-linked covalent bond with Asn.DO i have add some
      script in my carbohydrate.param or .top file to make
      covalent bond bet ND2 and C?.I would appreciate any
      help provided.

      Thanks
      Guru
      Florida State University
      Tallahassee















      __________________________________
      Do you Yahoo!?
      Win a $20,000 Career Makeover at Yahoo! HotJobs
      http://hotjobs.sweepstakes.yahoo.com/careermakeover
    • Mark A. White
      Guru, Here is an example of a Cys - HEME bond patch in generate.inp. Note that the connectivity and bond distance/angles are specified in the TOP and PARAM
      Message 2 of 4 , May 3, 2004
        Guru,

        Here is an example of a Cys - HEME bond patch in generate.inp. Note
        that the connectivity and bond distance/angles are specified in the TOP
        and PARAM files respectively. You probably only need to include the
        bond distance restraint in your patch. I hope this helps.

        Mark

        ### generate.inp ###
        {* any special ligand patches can be applied here *}
        {===>}
        {* Note: PRESidue CYHM lines are added *}
        {* at the end of the ligand topology file. *}
        {* This patch covalently bonds CYS 36 to HEM 501 *}
        patch cyhm
        reference=1=( resid 36 )
        reference=2=( resid 501 )
        end
        {<===}

        ### ligand.top ###
        MASS FE+3 55.84700 ! assuming FE -> 55.84700 + 1.008 * 0 (Hs)
        !------------------------------------------------------------------
        ! PATCH FOR CYSteine-HEMe LIGAND
        !------------------------------------------------------------------
        PRESidue CYHM ! Patch for HEME with a Cys ligand

        BOND 1SG 2FE+3
        ANGLe 1SG 2FE+3 2NA
        ANGLe 1SG 2FE+3 2NB
        ANGLe 1SG 2FE+3 2NC
        ANGLe 1SG 2FE+3 2ND
        ANGLe 1CB 1SG 2FE+3

        END {Residue PHEM}
        !------------------------------------------------------------------

        ### ligand.param ###
        bond FE+3 SH1E 500.0 2.27 ! SG over heme center
        angle SH1E FE+3 NZ2 100.0 98.0 ! SG over heme center
        angle SH1E FE+3 NZ3 100.0 98.0 ! SG over heme center
        angle SH1E FE+3 NZ4 100.0 98.0 ! SG over heme center
        angle SH1E FE+3 NZ5 100.0 98.0 ! SG over heme center




        laxmicantan gurunathan wrote:

        >Dear CNS users,
        >
        >I am having a problem in connecting the carbohydrate
        >moeity NAG(N-acetyl glucosamine) with the Asn residue
        >of my protein.I used the following script in the
        >generate.inp file but it did not give any covalent
        >linkage between the NAG & Asn.
        >
        >The refinement programme pushes the sugar from the
        >residue and yields non covalent distance between
        >ND2(Asn) and C (NAG).
        >
        >=========================== carbohydrate links
        >===========================}
        >
        >{* Select pairs of residues that are linked *}
        >{* First entry is the name of the patch residue. *}
        >{* Second and third entries are the resid and segid
        >for the atoms
        > referenced by "-" in the patch. *}
        >{* Fourth and fifth entries are the resid and segid
        >for the atoms
        > referenced by "+" in the patch *}
        >{+ table: rows=6 numbered
        > cols=6 "use" "patch name" "segid -" "resid
        >-" "segid
        >+" "resid +" +}
        >
        >{+ choice: true false +}
        >{===>} carbo_use_1= true;
        >{===>} carbo_patch_1="B1N";
        >{===>} carbo_i_segid_1="A"; carbo_i_resid_1=95;
        >{===>} carbo_j_segid_1="A"; carbo_j_resid_1=501;
        >
        >Here 95 refers to ASN and 501 refers to NAG.I have
        >only one carbohydrate residue and i need to have a
        >N-linked covalent bond with Asn.DO i have add some
        >script in my carbohydrate.param or .top file to make
        >covalent bond bet ND2 and C?.I would appreciate any
        >help provided.
        >
        >Thanks
        >Guru
        >Florida State University
        >Tallahassee
        >
        >
        >
        >
        >
        >
        >
        >
        >
        >
        >
        >
        >
        >
        >
        >__________________________________
        >Do you Yahoo!?
        >Win a $20,000 Career Makeover at Yahoo! HotJobs
        >http://hotjobs.sweepstakes.yahoo.com/careermakeover
        >
        >
        >
        >--------------------------------------------------------
        >List information at http://groups.yahoo.com/group/cnsbb.
        >Posting is only allowed for members of this list.
        >
        >
        >Yahoo! Groups Links
        >
        >
        >
        >
        >
        >
        >

        --

        Best Regards,

        Mark

        -_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_
        Mark A. White, Ph.D. Tel:
        Sealy Center for Structural Biology (409) 747-4747
        Dept. of Human Biological Chemistry & Genetics Fax:
        Basic Science Building, Room 660C (409) 747-4745
        University of Texas Medical Branch email:
        Galveston, TX 77555-0647 mailto://white@...
        http://xray.utmb.edu http://xray.utmb.edu/~white
        -_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_
      • Harry M. Greenblatt
        BS D ... The sugar (501) should be listed first, and then the protein residue. See if that fixes things. Harryt ... Harry M. Greenblatt Research Associate Dept
        Message 3 of 4 , May 4, 2004
          BS"D

          >
          > {+ choice: true false +}
          > {===>} carbo_use_1= true;
          > {===>} carbo_patch_1="B1N";
          > {===>} carbo_i_segid_1="A"; carbo_i_resid_1=95;
          > {===>} carbo_j_segid_1="A"; carbo_j_resid_1=501;
          >

          The sugar (501) should be listed first, and then the protein residue.
          See if that fixes things.
          Harryt

          ------------------------------------------------------------------------
          -------------------------
          Harry M. Greenblatt
          Research Associate
          Dept of Structural Biology harry.greenblatt@...
          Weizmann Institute of Science Phone: 972-8-934-3625
          Rehovot, 76100 Facsimile: 972-8-934-4159
          Israel
        Your message has been successfully submitted and would be delivered to recipients shortly.