Hello Qinhong--
> I'm using the newest Xplor-NIH 2.40. I meet problem when I tried to add
> atom-based parameter for my ligand. I follow the manual, here is an example:
> BOND ( name C3C and resname CYC ) ( name CAC and resname CYC ) 222.500 1.5292
> when I tried to generate an extended structure, the software complained
> parameters are missing for this bond. While it is all right when I applied
> type-based parameter. I don't know what's wrong in my sentence.
I don't see an obvious error in your bond parameter specification. How
are you applying it. Like this:
xplor.command("""param
BOND ( name C3C and resname CYC ) ( name CAC and resname CYC ) 222.500 1.5292
end""")
should work.
>
> The second question is, is there any way to put a rigid ligand into protein
> cavity, and keep the ligand rigid during simulated annealing? The reason we
> want
> to do this is, we already know the ligand conformation. But we don't have
> enough
> NOE to reach such conformation in a random simulated annealing. Thus we want
> to
> keep ligand rigid and let surrounding protein fit it--like a reversed docking.
> Can Xplor-NIH do that?
>
Certainly: use the IVM to group the ligand as a rigid body. So if you
have an IVM object dyn
dyn=IVM()
dyn.group("resname CYC")
protocol.torsionTopology(dyn)
Then, the ligand named CYC will remain rigid throughout the
calculation, while the protein will move in torsion angle space.
best regards--
Charles
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