Re: [AMBER] hexagonal unit cell for membrane simulation with NAMD

From: Pawel <>
Date: Fri, 08 Nov 2013 17:03:40 -0500

Hi Thomas,

Just to add to what Brian said, you can use AmberTool's AddToBox
program to create a hexagonal unit cell. Just make sure you specify
coordinates consistent with a hexagonal space group (a a c 90 90 120).
You can then also use PropPDB if you wish to create a model of several
hexagonal unit cells side by side (for a lipid membrane, just extend
them out in a and b not c directions). You can then simulate it in Amber
if you'd like which will treat this just like a triclinic cell (of which
a hexagonal cell is a special case). For NAMD, take a look at:

Section 4 details how to properly set the cellBasisVectors in NAMD
(although I think there is an error. If I'm not mistaken, the bottom
line of your crd/rst file should read

     d d h 90.0 90.0 120.0


     d d h 60.0 90.0 90.0

At least that's how it's worked for me in the past. Also take note of
the other information on that page. There's some intricacy to using
Amber in NAMD.


On 11/08/2013 09:32 AM, Brian Radak wrote:
> I'm not an expert on non-orthorhombic boxes, but I did once get AMBER to
> work correctly with a rhombic dodecahedron. The solution was to:
> 1) read a pdb of the water box into leap
> 2) use "setBox" to set dummy box information
> 3) edit the box vectors in the inpcrd by hand
> 4) edit IFBOX to be equal to 3 by hand in the prmtop
> I checked all of this by using the "image familiar" command in
> ptraj/cpptraj. However, be aware that AMBER will simulate in the triclinic
> representation, which will make it quite difficult to visualize what is
> actually going on. No guarantees on that working for sure though.
> Regards,
> Brian
> On Thu, Nov 7, 2013 at 7:37 PM, Thomas Evangelidis <>wrote:
>> Dear list,
>> Does anyone know if I can create a hexagonal membrane patch with lipid11 ff
>> to run a simulation in a hexagonal unit cell with NAMD? CHARMM-GUI provides
>> an option to create a hexagonal box but I think in the .prmtop file there
>> is a pointer named "IFBOX" which determines the box size, and since AMBER
>> does not support that kind of shape I suspect there might be a conflict
>> with the cell basis vectors in the NAMD configuration file. The same may
>> apply with the lattice vectors written in the last line of .inpcrd.
>> Other than that, the lipid11 tutorial states that I should choose a
>> Rectangular box type in CHARMM-GUI since this geometry is required for
>> constant surface tension. Will there be a problem if I choose a Hexagonal
>> box type and run the simulation in NAMD provided that I define correctly
>> the cell basis vectors?
>> Could anyone please clarify these points?
>> thanks,
>> Thomas
>> --
>> ======================================================================
>> Thomas Evangelidis
>> PhD student
>> University of Athens
>> Faculty of Pharmacy
>> Department of Pharmaceutical Chemistry
>> Panepistimioupoli-Zografou
>> 157 71 Athens
>> email:
>> website:
>> _______________________________________________
>> AMBER mailing list

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Received on Fri Nov 08 2013 - 14:30:02 PST
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