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

From: James Starlight <>
Date: Fri, 12 Sep 2014 13:07:51 +0200

Hi Callum,

This time I'm dealing with the preparation of big sets of membrane protein
simulation where I
1) copy lipids from some ref.pdb to each model.pdb
2) should add water to each system (using tleap for instance) and prepare
amber topology

(here all my models and ref have the same shape so I can use the shared
bi-layer with the same hole)
the problem is that some extra water is added to the X-Y plane during
solvation which I need to cut. I've tried to use some VMD script but it has
the problems between topologies which should also provided in that script
(below you can find it). If someone knows how to adapt it to amber it will
be perfect.

#vmd -e script.tcl
mol new amber_OR5AP2_MULTI.pdb
set all [atomselect top all]
$all set beta 0
set seltext "water and same residue as abs(z) < 25"
set sel [atomselect top $seltext]
$sel set beta 1
set badwater [atomselect top "water and beta > 0"]
set reslist [$badwater get resid]
foreach resid $reslist {
 delatom $resid
writepdb mol edited.pdb
#writeparm7 ! dont know how to specify this!
#write inpcrd ! dont know how to specify this!

All the best,


2014-09-12 12:47 GMT+02:00 Dickson, Callum J <>:

> 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.
> Cheers,
> Callum
> ________________________________________
> 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,
> James
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Received on Fri Sep 12 2014 - 04:30:02 PDT
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