As I understand, the cap potential is to add harmonic restrain if the cap
molecules go beyond a given radius for a given center. In this way, the
water molecule that goes too much away from the system, which results in
the failure of MD simulation in vacuum, can be avoid. Is my understanding
correct? If no, could you please give me some hints on finding related
references?
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.
Thanks!
Junjun
On Tue, Feb 7, 2012 at 3:35 AM, David A Case <case.biomaps.rutgers.edu>wrote:
> 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 - 18:30:03 PST
