On Mon, Aug 15, 2011, Fenley, Andrew wrote:
>
> I'm trying to create a topology file that preserves the
> following ordering: heavy atoms followed by hydrogens. I've tuned the
> input PDB to conform to all the atom naming conventions and there are
> no complaints from tleap regarding the structure. I can save a topology
> and inpcrd file, but in doing so, the atom ordering gets defaulted to
> the ordering in the templates. Is there a way to turn this off?
No.
> when adding explicit solvent and then ions to neutralize the system, do
> the ion atoms always come after the solute atoms in the topology file
> regardless if one adds the explicit solvent first then counter ions in
> tleap?
I don't know the answer off-hand, but can't you find out for yourself by just
trying it?
...dac
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Received on Tue Aug 16 2011 - 13:00:03 PDT
