Thanks for Ross' warmly reply. I have another question: can I set the
radius by edit the .prmtop file? This seems more simple...
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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Sep 03 2010 - 19:30:03 PDT
