Dear Berk,
you might want to wait for the next (very soon) release of AmberTools.
There, the FEW^mem workflow might do what you need: facilitate the setup
of molecular dynamics simulations with explicit membrane, and the setup
and execution of effective binding energy calculations according to a
1-trajectory implicit solvent/implicit membrane MM-PBSA approach for
multiple ligands binding to the same membrane protein.
Please see here for more details:
Biochimica et Biophysica Acta 1850 (2015) 972–982
Best regards
Holger
Am 05.05.2015 um 20:02 schrieb Ramin Ekhteiari:
> Hi Dears,
> I try to use MM_PBSA.py script to estimate delta free energy value between a ligand and a GPCR (membrane protein). but the problem is that, GPCRs are considered as membrane proteins and they share large hydrophobic domains which are embedded into the membrane bilayer, so this method how can work by applying dielectric constant for overall atoms of protein. Can we use this method for GPCRs as well as other proteins.
>
> I appreciate for any advice.
> Cheers,Berk.
>
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Received on Tue May 05 2015 - 12:00:02 PDT
