[gmx-users] Respect waters in crystallographic pdb file?

[Jorge Fernandez de Cossio Diaz]

Hi all,
I have a crystallographic PDB file which comes some waters molecules. I want to run an MD simulation which includes those water molecules. After generating the topology file (which includes the waters) and defining the box shape, I fill the box with solvent using genbox. At this point it becomes impossible to track down visually where the water molecules are. My question is if the file that genbox outputs still contains the crystallographic water molecules? Or are they replaced by the molecules added by genbox?
Thanks in advance. Best, cossio
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