1) the RADII section is for the intrinsic radius for the implicit
solvation calculations. it is not vdw radius.
2) the prmtop does not contain per-atom vdw parameters, only pointers
into the atom type arrays that hold the parameters. so, you can't
change 1 atom's parameters there, because you would have to change
them for all hydrogens of the same atom type.
3) it seems to me that you need to go back to the actual residue
library file and determine the atom type- some of the hydrogen atoms
in Amber's force fields already have zero for the vdw well depth (you
want that, not zero for radius). you need to check and see what it is,
and if it isn't zero then you will need to make a new residue file
with a different atom type that has zero for vdw interaction. it's not
as simple as modifying the prmtop.
On Sat, May 8, 2010 at 2:51 AM, Jeffrey <jeffry20072008.yahoo.cn> wrote:
> 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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>
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Received on Sat May 08 2010 - 03:30:03 PDT
