[AMBER] Protein Crystal Buried Waters and Amber Simulation ?

From: Christine Baranski <chbaranski.googlemail.com>
Date: Fri, 5 Mar 2010 00:04:16 +0000

Dear All,

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. 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.

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

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Received on Thu Mar 04 2010 - 16:30:02 PST
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