[gmx-users] protein and DMPC in Charmm36 ff

Tomek Wlodarski tomek.wlodarski at gmail.com
Sun Apr 15 19:09:16 CEST 2012


I would like to simulate protein in DMPC bilayer in Charmm36 ff.
I checked mailing list and KALP-15 tutorial, but still I have a few basic

1) I have problem with DMPC bilayer...

- VMD membrane builder only provides POPE and POPC lipids...

- on the Peter Tieleman page there is a pdb but with different atom names
and without H, of course I can rename atoms but pdb2gmx would not
regenerate hydrogens - lipids.hdb file is empty

- I have found also this page:
http://terpconnect.umd.edu/~jbklauda/research/download.html and it works
but I am not able to extend bilayer with genconf... I always end up with
separated copies of starting patch... even with -dist 0 0 0.

2) How to choose proper lipid patch size and simulation box size? For
globular proteins I would just run editconf with -bt dodecahedron -d 1. How
it is done in membrane protein simulation?

Thanks a lot for any help and suggestions.

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