Re: [AMBER] Protein Crystal Buried Waters and Amber Simulation ?

From: Bill Ross <>
Date: Thu, 4 Mar 2010 16:14:07 -0800 (PST)

> I want to run a simulation on a PDB structure. I want to know how I can find
> which waters molecule I should keep in simulation and which should delete?
> or I should keep all the waters.

Will you be solvating? If so, I would keep all the waters.
Otherwise, it seems that deleting any would be a judgement
process for each water in the model, unless you just decided
to delete all. Overall, I would lean toward a solvated simulation
keeping all existing waters and adding a box or truncated
octahedron of waters with e.g. a 10A clearance.

> Further I would like to ask do I need to
> add hydrogen atoms into the PDB file before simulation or tleap can do this
> for me.

tleap can do it for you.

> Is there any tool/script available by which I can find water molecules
> buried in multiple proteins files?

Possibly apropos, to get rid of all waters with residue name WAT, you can

% egrep -v WAT start.pdb > dehyd.pdb

Ideally there would be an option in xleap to highlight residues by name.
Maybe it's there - I haven't used leap in years.


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Received on Thu Mar 04 2010 - 16:30:05 PST
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