[ccp4bb]: Carbohydrate patch in CNS

["Harry M. Greenblatt" <harry.greenblatt@weizmann.ac.il>]

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BS"D

  I  answered Filip privately about how to get CNS to recognise a bond
between an ASN and a Glc-NAc, but there have been one or two messages in
reply which have suggested having to make a *special* patch for the
bond.  It seems that not everyone is aware that the patch is already
predifined in CNS, and one merely has to fill in the correct section of
generate.inp:

{=========================== 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_1=59;
{===>} carbo_j_segid_1="A"; carbo_j_resid_1=59;


  The line "carbo_patch_1" is what tells CNS the type of bond topologies
and parameters to use.  No further patches are required.  One must, of
course, include the the CNS_TOPPAR:carbohydrate.top and
CNS_TOPPAR:carbohydrate.param files in generate.inp and the .param file
in the anneal.inp or whatever refinement/map protocol you use. 

HMG
-- 
------------------------------------------------------------------------
  Harry M. Greenblatt           | Phone: 972-8-934-3625
  Research Assistant            | FAX  :           4159
  Dept. of Structural Biology   |
  Weizmann Institute of Science |
  Rehovot, Israel 76100         | Email: harry.greenblatt@weizmann.ac.il
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