[gmx-users] analysis of membrane protein

Justin A. Lemkul jalemkul at vt.edu
Fri Sep 4 12:23:23 CEST 2009

Samik Bhattacharya wrote:
> hi all,
> i have simulated a membrane protein system in DPPC and DMPC bilayer. i 
> have got the trajectories and analysed them with the gromacs tools. now 
> i want to get the bonding connectivity of the protein with that of the 
> lipid layer. can i get that graphically (i.e. in xvg format) ? is there 
> any option to visualize the protein - lipid connections other than ngmx? 
> as the system is big enough i cant get a clear idea about the bonding 
> patterns of the protein with the lipid bilayer....waiting for 
> suggestions....

Bonds don't exist between lipids and proteins, unless you've specified them in 
the topology.  And if you've done that, you should at least have some idea of 
the relevant atom numbers, so you can use tools like g_bond and g_angle with 
special index groups.


> Thank You all
> 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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