On Tue, Feb 07, 2012, liu junjun wrote:
>
> The water molecules in my PDB files surround the protein, making the system
> a spherical shape. Actually, I am doing a post-process on an optimized
> structure and focus on just few part of the system.
In this case, you can just add the cap information in the sander input file.
But it is far from easy to get the proper potential, such that you don't force
waters too close to the protein, or allow them to drift too far away, leaving
"bubbles" behind. The cap option was added maybe 30 years ago, but is almost
never used (at least by developers that I know of). So, proceed with caution.
....dac
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Received on Tue Feb 07 2012 - 17:30:03 PST
