On Tue, 2014-05-06 at 14:15 +0400, James Starlight wrote:
> Dear Amber Users!
>
>
> I'm looking for the tutorial with step-by-step workflow of the construction
> of membrane-protein system having pre-equilibrated bilayer and protein in
> separate pdb's.
> Also I'll be thankful if you provide me with some online service wich could
> do such taks automaticly (like charm-gui membrane builed for instance).
Why not just use CHARMM GUI membrane builder? Or the one in VMD? In
fact, the Amber lipid tutorial (shown below) suggests the CHARMM-GUI
builder. There's a script "charmmlipid2amber.x" (soon to be updated
with a more extensive "charmmlipid2amber.py") script that will convert
all of the CHARMM lipid residues into corresponding Amber residues.
Then you can use that PDB file with lipid14 and ff14SB to parametrize
your system.
As for the tutorial, see
http://ambermd.org/tutorials/advanced/tutorial16/An_Amber_Lipid_Force_Field_Tutorial.html
There's nothing I know of that shows how to insert a membrane-bound
protein, but the hard part would be setup. Presumably the CHARMM GUI
lipid builder allows you to build such a system, then all you have to do
is load the appropriate protein force field (and possibly make sure atom
names match).
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue May 06 2014 - 05:00:02 PDT
