[gmx-users] protein and DMPC in Charmm36 ff

Krzysztof Kuczera kkuczera at ku.edu
Mon Apr 16 17:19:21 CEST 2012

An easy way to build a protein in a bilayer is through the charmm-gui 
Partial drawbacks are that you need CHARMM to perform final equilibration
and then may need to rename some atoms to work with GROMACS
On plus side is that charmm36.ff retains the original CHARMM atom names 
in the lipids
Krzysztof Kuczera

On 4/15/12 12:09 PM, 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
> - I have found also this page: 
> http://terpconnect.umd.edu/~jbklauda/research/download.html 
> <http://terpconnect.umd.edu/%7Ejbklauda/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.
> Best!
> tomek

Krzysztof Kuczera
Departments of Chemistry and Molecular Biosciences
The University of Kansas
2010 Malott Hall
Lawrence, KS 66045
Tel: 785-864-5060 Fax: 785-864-5396 email: kkuczera at ku.edu

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