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how many carbohydrates can CNS 1.1 link?

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  • Dai, Shaodong
    Hi everyone, I have a protein dimer with 12 carbohydrates bound. But it seems generate.inp can only deal with 6 sugars and always add oxygen to the rest. Is
    Message 1 of 2 , Mar 1, 2006
      Hi everyone,


      I have a protein dimer with 12 carbohydrates bound. But it seems generate.inp can only deal with 6 sugars and always add oxygen to the rest. Is it some problems with my input file or a bug with CNS 1.1? I have tried different numbering and segid and switch around the order, but none helped. Any suggestion would be appreciated.



      Sincerely,

      Shaodong

      {=========================== 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="G"; carbo_i_resid_3=602;
      {===>} carbo_j_segid_1="D"; carbo_j_resid_3=118;
      {+ choice: true false +}
      {===>} carbo_use_2=true;
      {===>} carbo_patch_2="B14";
      {===>} carbo_i_segid_2="G"; carbo_i_resid_4=601;
      {===>} carbo_j_segid_2="G"; carbo_j_resid_4=602;
      {+ choice: true false +}
      {===>} carbo_use_3=true;
      {===>} carbo_patch_3="B1N";
      {===>} carbo_i_segid_3="G"; carbo_i_resid_5=603;
      {===>} carbo_j_segid_3="E"; carbo_j_resid_5=19;
      {+ choice: true false +}
      {===>} carbo_use_4=true;
      {===>} carbo_patch_4="B14";
      {===>} carbo_i_segid_4="G"; carbo_i_resid_6=604;
      {===>} carbo_j_segid_4="G"; carbo_j_resid_6=603;
      {+ choice: true false +}
      {===>} carbo_use_5=true;
      {===>} carbo_patch_5="B1N";
      {===>} carbo_i_segid_5="B"; carbo_i_resid_1=606;
      {===>} carbo_j_segid_5="A"; carbo_j_resid_1=78;
      {+ choice: true false +}
      {===>} carbo_use_6=true;
      {===>} carbo_patch_6="B14";
      {===>} carbo_i_segid_6="B"; carbo_i_resid_2=605;
      {===>} carbo_j_segid_6="B"; carbo_j_resid_2=606;
      {+ choice: true false +}
      {===>} carbo_use_7=true;
      {===>} carbo_patch_7="B1N";
      {===>} carbo_i_segid_7="B"; carbo_i_resid_5=608;
      {===>} carbo_j_segid_7="B"; carbo_j_resid_5=19;
      {+ choice: true false +}
      {===>} carbo_use_8=true;
      {===>} carbo_patch_8="B14";
      {===>} carbo_i_segid_8="B"; carbo_i_resid_6=607;
      {===>} carbo_j_segid_8="B"; carbo_j_resid_6=608;
      {===>} carbo_use_9=true;
      {===>} carbo_patch_9="B1N";
      {===>} carbo_i_segid_9="B"; carbo_i_resid_1=610;
      {===>} carbo_j_segid_9="A"; carbo_j_resid_1=118;
      {+ choice: true false +}
      {===>} carbo_use_10=true;
      {===>} carbo_patch_10="B14";
      {===>} carbo_i_segid_10="B"; carbo_i_resid_2=609;
      {===>} carbo_j_segid_10="B"; carbo_j_resid_2=610;
      {+ choice: true false +}
      {===>} carbo_use_11=true;
      {===>} carbo_patch_11="B1N";
      {===>} carbo_i_segid_11="G"; carbo_i_resid_1=612;
      {===>} carbo_j_segid_11="D"; carbo_j_resid_1=78;

      {+ choice: true false +}
      {===>} carbo_use_12=true;
      {===>} carbo_patch_12="B14";
      {===>} carbo_i_segid_12="G"; carbo_i_resid_3=611;
      {===>} carbo_j_segid_12="G"; carbo_j_resid_3=612;


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    • Aalt-Jan van Dijk
      hi Shaodong, I think you have to correct the carbo_i_resid_?=??? and carbo_j_resid_?=??? entries: now they are randomly numbered; they should start at 1 and be
      Message 2 of 2 , Mar 2, 2006
        hi Shaodong,

        I think you have to correct the carbo_i_resid_?=???
        and
        carbo_j_resid_?=??? entries: now they are randomly
        numbered; they should start at 1 and be numbered
        continuously (just like carbo_i_segid_? and
        carbo_j_segid_?). So first one should be:

        carbo_i_resid_1=602;
        carbo_j_resid_1=118;

        and last one:

        carbo_i_resid_12=611;
        carbo_j_resid_12=612;

        Aalt-Jan

        --- "Dai, Shaodong" <dais@...> wrote:

        > Hi everyone,
        >
        >
        > I have a protein dimer with 12 carbohydrates bound.
        > But it seems generate.inp can only deal with 6
        > sugars and always add oxygen to the rest. Is it
        > some problems with my input file or a bug with CNS
        > 1.1? I have tried different numbering and segid and
        > switch around the order, but none helped. Any
        > suggestion would be appreciated.
        >
        >
        >
        > Sincerely,
        >
        > Shaodong
        >
        > {=========================== 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="G"; carbo_i_resid_3=602;
        > {===>} carbo_j_segid_1="D"; carbo_j_resid_3=118;
        > {+ choice: true false +}
        > {===>} carbo_use_2=true;
        > {===>} carbo_patch_2="B14";
        > {===>} carbo_i_segid_2="G"; carbo_i_resid_4=601;
        > {===>} carbo_j_segid_2="G"; carbo_j_resid_4=602;
        > {+ choice: true false +}
        > {===>} carbo_use_3=true;
        > {===>} carbo_patch_3="B1N";
        > {===>} carbo_i_segid_3="G"; carbo_i_resid_5=603;
        > {===>} carbo_j_segid_3="E"; carbo_j_resid_5=19;
        > {+ choice: true false +}
        > {===>} carbo_use_4=true;
        > {===>} carbo_patch_4="B14";
        > {===>} carbo_i_segid_4="G"; carbo_i_resid_6=604;
        > {===>} carbo_j_segid_4="G"; carbo_j_resid_6=603;
        > {+ choice: true false +}
        > {===>} carbo_use_5=true;
        > {===>} carbo_patch_5="B1N";
        > {===>} carbo_i_segid_5="B"; carbo_i_resid_1=606;
        > {===>} carbo_j_segid_5="A"; carbo_j_resid_1=78;
        > {+ choice: true false +}
        > {===>} carbo_use_6=true;
        > {===>} carbo_patch_6="B14";
        > {===>} carbo_i_segid_6="B"; carbo_i_resid_2=605;
        > {===>} carbo_j_segid_6="B"; carbo_j_resid_2=606;
        > {+ choice: true false +}
        > {===>} carbo_use_7=true;
        > {===>} carbo_patch_7="B1N";
        > {===>} carbo_i_segid_7="B"; carbo_i_resid_5=608;
        > {===>} carbo_j_segid_7="B"; carbo_j_resid_5=19;
        > {+ choice: true false +}
        > {===>} carbo_use_8=true;
        > {===>} carbo_patch_8="B14";
        > {===>} carbo_i_segid_8="B"; carbo_i_resid_6=607;
        > {===>} carbo_j_segid_8="B"; carbo_j_resid_6=608;
        > {===>} carbo_use_9=true;
        > {===>} carbo_patch_9="B1N";
        > {===>} carbo_i_segid_9="B"; carbo_i_resid_1=610;
        > {===>} carbo_j_segid_9="A"; carbo_j_resid_1=118;
        > {+ choice: true false +}
        > {===>} carbo_use_10=true;
        > {===>} carbo_patch_10="B14";
        > {===>} carbo_i_segid_10="B"; carbo_i_resid_2=609;
        > {===>} carbo_j_segid_10="B"; carbo_j_resid_2=610;
        > {+ choice: true false +}
        > {===>} carbo_use_11=true;
        > {===>} carbo_patch_11="B1N";
        > {===>} carbo_i_segid_11="G"; carbo_i_resid_1=612;
        > {===>} carbo_j_segid_11="D"; carbo_j_resid_1=78;
        >
        > {+ choice: true false +}
        > {===>} carbo_use_12=true;
        > {===>} carbo_patch_12="B14";
        > {===>} carbo_i_segid_12="G"; carbo_i_resid_3=611;
        > {===>} carbo_j_segid_12="G"; carbo_j_resid_3=612;
        >
        >
        > CONFIDENTIALITY NOTICE: The information contained in
        > this message is legally privileged and confidential
        > information intended for the use of the individual
        > or entity named above. If the reader of this message
        > is not the intended recipient, or the employee or
        > agent responsible to deliver it to the intended
        > recipient, you are hereby notified that any release,
        > dissemination, distribution, or copying of this
        > communication is strictly prohibited. If you have
        > received this communication in error, please notify
        > the author immediately by replying to this message
        > and delete the original message. Thank you.
        >
        >
        >
        >


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