change caused by the parameter file

Axel T. Brunger brunger at LAPLACE.CSB.YALE.EDU
Mon Nov 25 16:35:47 EST 1996


The new parameters use different van der Waals radii (very similar
to PROLSQ).  These differences mainly affect the 1-4 interactions.  
However, since the solvent mask calculation uses the van der Waals
parameters
the mask will be different.  You may have to use a different probe
radius when computing the mask.  


   Axel Brunger

Jinsong Liu wrote:
> 
> When I used the new parameter file: protein_rep.param and calculated the bulk
> solvent correction by setup_bulksol.inp, I found that things changed. For example, average mask radius changed from 2.0A to 1.7A, volume outside mask changed
> from 27% to 37%, and R( and Free)-factor changed by about 1%.
> I used to use parhcsdx.pro even in X-PLOR 3.854. I just happended to use the
> protein_rep.param and realized the changes.
> 
> Anyone has similar experience and can explain why the solvent volume changed
> so much?
> 
> Thanks.
> 
> jinsong

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| Axel T. Brunger          Dept. Molecular Biophysics and Biochemistry|
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