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Specifying a new bond type in X-plor

Felix F. Vajdos felix at alta.med.utah.edu
Sat Nov 22 19:10:40 EST 1997

Hello All,

A colleague of mine is currently refining a structure of a complex in
which two protein chains are linked by a thio-hemiacetal linkage.  This
is a covalent bond between a cysteine side-chain and the aldehyde form
of the carboxyl-terminus of another protein.  How might we specify a new
bond between the two groups?  He has succeeded in specifying a patch
statement for the bond, which seems to do okay during the generate
stage.  However, successive jobs complain that there are no
Lennard-Jones potentials for the groups.  My quick fix is to simply
remove the offending groups from the energy potential with the
constraints interaction statement, but we would ultimately like to treat
the covalent attachment in  a more elegant fashion.  Any suggestions?

Felix F. Vajdos
Dept. of Biochemistry
University of Utah
Salt Lake City, UT  84132

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