[gmx-users] membrane protein simulation

Justin A. Lemkul jalemkul at vt.edu
Fri May 29 13:19:49 CEST 2009

Samik Bhattacharya wrote:
> hi  i'm new to gromacs and want to simulate a protein inside a 
> phospholipid envelop (may be box or dodecahedron). for this i got the 
> pdb files of both the proteins and the lipids(e.g.POPC, POPE etc). but 
> i'm facing a lot of problems in generating the topology files as well as 
> in running grompp as gromacs does not support lipids. i also tested it 
> by using the lipid.itp file in the top directory. can anyone suggest me 
> any tutorial where i can find detailed discussion on this matter? and 
> obviously some help in how to go for it??

Yes, there is a tutorial here:



> Thanking you in advance
> Shamik
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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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