On Fri, Sep 3, 2010 at 10:24 PM, Anbang Li <lianbang.gmail.com> wrote:
> Thanks for Ross' warmly reply. I have another question: can I set the
> radius by edit the .prmtop file? This seems more simple...
>
The radius in the RADII section only affects the implicit solvent
calculations. The VDW radii are hidden in the combining rules in the
LENNARD_JONES_A/BCOEF arrays. I've written a script that will extract them,
allow you to change them, then rewrite the prmtop file, but the easiest
thing to do would probably be define the VDW radius in an frcmod file and
load it into leap that way.
Hope this helps,
Jason
> Thanks,
> Li
>
> 2010/9/4, Bill Ross <ross.cgl.ucsf.edu>:
> > > > I totallly have no idea to set its radius!
> > >
> > > The atom type from the .lib is looked up in parmXXX.dat or .frcmod
> files
> > > in the nonbonded parameter section. So pick an atom type and then if
> it's
> > > a new one make a .frcmod with the R* and epsilon parameters in it and
> > > load that too (loadamberparams cmd or similar).
> >
> > More background: charge is different for every atom, so it is set
> > in the atom definition in the residue in .lib. All other parameters
> > are generic to many atoms of the same type, so these are stored in
> > the parm.dat or frcmod files according to atom type, which is more
> > general than charge.
>
> --
> Anbang LI
> Physics Department, HuaZhong Normal University, China
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Fri Sep 03 2010 - 21:00:03 PDT
