Thanks Jason,
If I understood you correctly there is charmmlipid2amber script which is
useful for the conversion of pdb made by charm-gui including full complex
consisted of protein embedded in the solvated bi-layer, isn't it? So during
preparaton of such system having converted pdb I only should provide for
tleap lipid14 (for lipids), amber99sb (protein) and Cgenff (for ligand)
params, shouldn't it?
James
2014-05-06 15:57 GMT+04:00 Jason Swails <jason.swails.gmail.com>:
> 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 Thu May 08 2014 - 00:30:02 PDT
