Hi Jeffrey,
maybe could be of your interest to check H++ server.
http://biophysics.cs.vt.edu/H++/
also this discussion thread might be interesting for you:
http://archive.ambermd.org/201004/0473.html
Best,
Marek
Dne Sat, 08 May 2010 08:51:02 +0200 Jeffrey <jeffry20072008.yahoo.cn>
napsal/-a:
> Dear AMBER users,
> We are going to calculate the pka of a protonation of residue in a
> protein model, following the tutorial at
> http://ambermd.org/tutorials/advanced/tutorial6/. I disabled the vdw
> interaction by setting the vdw radii of the hydrogen atom to 0.0 in the
> prmtop file (the term under %FLAG RADII). But it is strange that the vdw
> interaction didn't change w/o modification of the radii.
> I am not sure whether I did it correctly or not and so request your
> suggestions.
> Many thanks.
> Jeffrey Yang
>
>
>
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Received on Sat May 08 2010 - 15:30:03 PDT
