On Mon, Feb 06, 2012, liu junjun wrote:
>
> The solvateCap command in LEap program is to add more water molecules into
> the system which will be cap molecules. But I have some water molecules
> already existing in my PDB file. I want these existing waters to be cap
> molecules but don't want any added molecules. Is it possible? How to set
> the existing waters to be the cap molecules?
Sounds like you don't want a cap potential at all. Note that the water cap is
not often used by people running Amber. But you would definitely need to add
waters to a pdb structure to obtain the "cap": it would not make sense to just
use the existing crystallographic waters.
....dac
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Received on Mon Feb 06 2012 - 12:00:02 PST
