On 8/17/15 1:42 PM, Jorge Fernandez de Cossio Diaz wrote:
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
They should be in the same place they always were (unless you've modified the box dimensions, in which case the coordinates of everything get changed). But genbox shouldn't delete waters that were already present. The crystallographic waters should always be the first ones written after e.g. the protein.
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