[gmx-users] protein and DMPC in Charmm36 ff

Justin A. Lemkul jalemkul at vt.edu
Sun Apr 15 19:51:13 CEST 2012

Tomek Wlodarski wrote:
> Hi,
> 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 questions.
> 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

You can create a lipids.hdb entry for this purpose.  It will be quite 
repetitive, but pretty easy.

> - 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.

The .pdb files do not have boxes that are recognized by editconf and thus it 
assigns zero as the box vector.  Generating a new box with editconf -d is based 
on the distance between atoms with the largest and smallest coordinates, which 
does not yield a satisfactory box (it is too large for the membrane itself). 
Thus you would have to assign a box manually for this to work.  I don't know of 
any truly efficient means of doing this.

> 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?

You need a similar though process.  The system should be large enough to prevent 
spurious PBC interactions.  The necessary size will be dictated by the size of 
the protein to be embedded.  The number of lipids may be a consideration as well 
if you are interested in membrane properties during the simulation.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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