[gmx-users] Removing water molecules from inside of the protein

Justin A. Lemkul jalemkul at vt.edu
Thu Nov 20 23:06:20 CET 2008

DimitryASuplatov wrote:
> Hello,
> recently after adding spc water to a structure I have notice that the
> molecules have been added to internal cavities. Even though this
> situation is possible, for example water could get inside during
> folding, this could cause artificial movement of aminoacids being
> pushed from inside by internal water. I have also noticed that if I
> trjconv gro file to pdb (for use in pymol editor) all solvent
> identificators change and that makes them untraceable.
> Is there a known program to remove internal solvent molecules? Do you
> think its crucial?

You can get rid of them with a text editor, if you know their residue numbers, 
or change the VDW radius of C or N slightly to try to exclude more water during 
the genbox stage.

Also, editconf is better suited for .gro-->.pdb conversion (and vice versa).


> Thanks.
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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