Hello Everyone,
As interest in membrane protein simulations have increased recently in the mailing list I've decided to write-up and share an optimized protocol to build AMBER compatible systems using a free version of Schrodinger's Maestro. At the time of writing this email, only homogeneous POPC membranes are supported. However, users are encouraged to submit their own charmmlipid2amber.py conversion rulesets.
The tutorial can be found here: https://github.com/ParkerdeWaal/AMBER-Maestro-lipid-tutorial
In contrast to that of the CHARMM web GUI and VMD membrane system routes, this tutorial provides a very straight GUI oriented approach to build AMBER compatible membrane system PDB files with relative ease and speed. Additionally, while written for membrane proteins, this tutorial can also be applied to soluble proteins as well with minor modifications.
Input and feedback are greatly appreciated.
Best,
Parker
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Received on Sat Jun 13 2015 - 18:30:03 PDT
