[gmx-users] Remove water from membrane protein

[Justin A. Lemkul]

Alex wrote:
> Dear all,
> I've inserted a protein in a DPPC layer and then I've solvated (after 
> modifying vdwradii.dat to avoid putting waters in wrong places).
> How can I check and eventually remove waters still being in wrong places?
> I've tried to load it in PdbViewer and in rasmol, but is veruy difficult to 
> distinguish waters in bilayer cavities.
> I'd like some practical suggestion.
> 

If the rendering is difficult, use a different rendering scheme or different 
program altogether :)

To remove waters, see:

http://www.gromacs.org/Documentation/How-tos/Membrane_Simulations

-Justin

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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