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:
http://ambermd.org/namd/namd_amber.html
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
not
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.
Pawel
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 <tevang3.gmail.com>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
>> GREECE
>>
>> email: tevang.pharm.uoa.gr
>>
>> tevang3.gmail.com
>>
>>
>> website: https://sites.google.com/site/thomasevangelidishomepage/
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Fri Nov 08 2013 - 14:30:02 PST
