[gmx-users] transmembrane protein simulation

Krzysztof Mlynarczyk mitomaster at gmail.com
Mon Jan 24 11:25:27 CET 2011


Yes, g_membed is the right tool for you. Please read the paper Wolf et al, J
Comp Chem, 31 (2010) 2169-2174. You will find a detailed description of the
insertion method and a quick manual. It will save you a lot of headache.


2011/1/24 Mohana lakshmi <mohanaa.bioinfo at gmail.com>

> Dear all
>     I am trying to run simulation of transmembrane protein, i am looking
> for better ways to setup protein with lipid membrane. initially i used VMD
> to insert protein with lipid membrane but it did not come out well, i got
> errors while running position restraint.  i read about g_membed tool in
> gromacs, is it helpful for setting up transmembrane proteins also?  Is there
> any other better ways to insert protein perfectly into the membrane?  Please
> help me to overcome this problem.....
> Thanks and regards
> --
> Mohanalakshmi N
> --
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