nitu sharma wrote:
Dear all
I have done successfully simulation of membrane protein , but after
that to visualise my final model clearly I have to remove water
molecules from my system (protein+lipid+water).
But I have no Idea about the which command I should use to do this even
it doesn't mentioned in justin,s tutorial also to make final pdb after
simulation.
So can anyone suggest me how to remove water form my final simulation
system to make final pdb of only protein and lipid molecule?
You asked a very similar question a few days ago, which I answered then.
http://oldwww.gromacs.org/pipermail/gmx-users/2009-June/042525.html You
want to extract a non-standard group (i.e. non-solvent), so you need to
make an index file that defines that group.
Mark
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