Re: [AMBER] Solvation and processing of lipid bilayers using tleap

From: Dickson, Callum J <>
Date: Fri, 12 Sep 2014 10:47:49 +0000

Hi James,

Is it not possible to prepare your system using the charmm membrane builder? You can then convert the pdb to amber format using the charmmlipid2amber script. Alternatively there is a membrane plugin in vmd or you could try packmol. As yet there are not suitable tools available in leap to build solvated bilayers.


From: James Starlight []
Sent: 11 September 2014 22:02
To: AMBER Mailing List
Subject: [AMBER] Solvation and processing of lipid bilayers using tleap

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,

AMBER mailing list

AMBER mailing list
Received on Fri Sep 12 2014 - 04:00:03 PDT
Custom Search