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

DimitryASuplatov genesup at gmail.com
Thu Nov 20 21:36:03 CET 2008

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?


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