[gmx-users] proceed from output of MD

[Ewaru]

Hi,

I have run a 20ns MD simulation on my protein structure and about to proceed
with Autodock. I am wondering if I have missed anything. The output of the
file is gro, so I converted it to a pdb file. Then, when I process it with
Autodock Tools, all I get is the water molecules surrounding my protein in a
box. How can I get rid of the box?

Please advice.

Thanking you in advance.


Best regards



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