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how to refine a covalent-bond inhibior?

=?UNKNOWN?Q?=A9P=AEa=A5=E0?= fencing at GATE.SINICA.EDU.TW
Tue Oct 27 13:12:11 EST 1998

Dear X-Plor newsgroup readers:

The protein I study is a enzyme-inhibitor complex.
This inhibitor is a covalent bonded inhibitor.
I generate it's topology and parameter file myself and
It is the same with the result generated on XPLO2D web server.
I use 'patch' command to link enzyme (His ND1) and inhibitor (BRP C1)
and then modify HIS to HISE ( let ND1 deprotoned),
There is no error information in molecule generation output file.
After conventional refinement, inhibitor molecule will distrot,
bond length and angle will unnormal ( ex. C1-C2 distance will change to
at least 2.6A, or some atoms maybe  too close ...... )
But if I don't link them, refinement will normal work , Rfree/R can be
decreased and inhibitor molecule is also at normal geometrical restraint

Could anybody tell me what's wrong and how to resolve this problem ?


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