[Xplor-nih] structure of protein with ligand

[Charles at Schwieters.org]

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Hello Irina--

> 
> I have built my small molecule with XPLOR, so now I have both psf and pdb 
> files.
> 
> In general,  to perform a simulated annealing for the complex of protein and 
> small molecule do I have to keep a small molecule rigid to get it in proper 
> orientation and without distorsion of its structure?

this is a bit of a judgement call on your part. I'd definitely keep
rigid those portions for which you know the geometry. If the molecule
contains rotatable bonds, but you have a good idea of its configuration,
fix the geometry. In any case, you might perform initial calculations
with a rigid conformation.

I hope this helps--
Charles
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