> > 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.
Bill
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Received on Fri Sep 03 2010 - 17:00:05 PDT
