Re: [AMBER] Radii in prmtop

From: Ray Luo <rayhuangluo.gmail.com>
Date: Sun, 29 Apr 2012 14:52:10 -0700

Note that the solvation radius is NOT LJ radius. These are totally different concepts. So the solvation radii are in a completely different section of the prmtop file, Dave meant the radii in this section are used when radiopt = 0, not those in the LJ coefficient sections.

Ray

--
Ray Luo, Ph.D.
On Apr 29, 2012, at 11:19 AM, Jesper Sørensen <jesorensen.ucsd.edu> wrote:
> Hi Dave,
> 
> Thanks for the answer, that clears some things up.
> I am still not clear on which radii PBSA uses, because if you set radiopt=0, does it then use the "RADII" or the radii based on the A and B coefficients?
>> %FLAG LENNARD_JONES_ACOEF
> 
> 
> Maybe others know this answer too?
> 
> Best,
> Jesper
> 
> On Apr 28, 2012, at 7:25 PM, case wrote:
> 
>>> 
>>> What does PBSA do when you supply it with a prmtop file? Use the vdW
>>> radii or the "intrinsic electrostatic radii" (unless of course you ask
>>> it for TYL06 radii).
>> 
>> Depends on the radiopt parameter; when radiopt=0, it uses whatever radii are in
>> the prmtop file.
> 
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Received on Sun Apr 29 2012 - 15:00:04 PDT