[AMBER] Solvation and processing of lipid bilayers using tleap

From: James Starlight <jmsstarlight.gmail.com>
Date: Fri, 12 Sep 2014 01:02:08 +0400

Dear Ambe users!

As I wrote previusly I've faced with the problem of the solvation of the
lipid bilayers using solvatebox command in tleap because some extra (in x-y
plane) water have been added after such processing. I'll be thankful if
someone share with me with some simple script which could cut extra water
based on chosen geometric criteriums from the processed systems. Also I'll
be happy to gain any suggestions from anyone who have deal with the same
problem and found possible sollutins including proper algorithms of
equilibrations (e.g application of the constant surface tension or
 external forces to push water from the bilayer)

Thanks for help,

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Received on Thu Sep 11 2014 - 14:30:02 PDT
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