Hi Marawan,
No, we have not done any membrane protein simulations with the gafflipid parameters as yet.
To the best of my knowledge, the easiest way to construct a membrane protein system would be to use the charmm membrane builder gui:
http://www.charmm-gui.org/?doc=input/membrane
You can then convert your system to lipid11 using the charmmlipid2amber.x script and run using a surface tension that reproduces experimental area per lipid. Membrane simulations in amber are in 3D using full periodic boundary conditions.
Work is currently under way to update the lipid11 parameters in amber.
Kind regards,
Callum
________________________________________
From: amber-bounces.ambermd.org [amber-bounces.ambermd.org] on behalf of marawan hussain [marawanhussain.yahoo.com]
Sent: 08 April 2013 04:49
To: AMBER List
Subject: [AMBER] GAFFlipid forcefield
Dear AMBER developers,
I’m interested in working with Lipid membrane simulation and
have recently read your interesting Soft Matter paper about GAFFlipid and I have
some quick questions:
1-Did
you simulate this in conjunction with a membrane protein like GPCR’s to see the
effect.?
2-I
have downloaded the parameters to play around with, the membrane does not have
holes, is it a good idea to insert it manually then let the system equilibrate with
time by minimization.?
3-As
I can understand, you simulate in a normal Periodic Boundary Conditions not in
the 2D phase space, is it true, if I understand it right, is it physically
sensible to do membrane simulation in 3D
space.?
4-Any
plan to include this in the normal Lipid11 forcefield soon, or I need to use
the coordinates and the parameters supplied for now.?
Full
of respect
Marawan
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Received on Mon Apr 08 2013 - 05:30:03 PDT
