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?
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