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? If anyone can help me I willbe really thankful for him/her. Nitu Sharma. Jawaherlal Nehru University New Delhi , India.
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