On Tue, May 07, 2013, seçkin Boz wrote:
>
> I define atom types using this command line:
>
> >parmchk -i $mol2File -f mol2 -o $frcMod
>
> HO 0.0000 0.0000 same as ho
Note that atom type HO has zero LJ parameters.
> Since I'm a biologist, developing a force field is far beyond my
> skills,
This is understandable, but you are not going to be able to explore different
tautomers without learning how to make new force fields, since Amber (at
least) has no existing force fields for the molecules you are interested in.
Given the constraints you mention, I'm not sure what the solution is. Are you
sure you need to do gas-phase molecular dynamics? Most studies of
tautomerization use quantum chemistry calculations, avoiding the need to
create new force fields.
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue May 07 2013 - 06:00:04 PDT
