AMBER: AMBER hydrophobic Box : script

From: Sophie Barbe <>
Date: Wed, 14 Mar 2007 11:48:50 +0100

Dear amber users,

I want to create a hydrophobic solvent box, especially octane to mimick the
hydrophobic environment of a protein.
For this purpose :
- I optimized Octane to the 6-31G* theory level
- I created the prep and frcmod files
- I solvated the stucture by itself
- I performed a constant volume MD run from 100 to 300K
- I performed a constant pressure MD run at 310K

For the next step, I need a script that goes through each solvent molecule in
the box and calculate if any are overlapping or to close to the solute. If it
finds an atom too close or overlapping the script shpuld then delete
 the solvent molecule. I would like to know if someone has already write a
script like that or can say to me where I can find a such script or a close

Thank you very much for your help

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Received on Sun Mar 18 2007 - 06:07:05 PDT
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