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

Johnny Lu johnny.lu128 at gmail.com
Mon Aug 17 20:09:04 CEST 2015

I haven't tried that before.
May be you can open the .gro files before and after genbox with a text
Then, check those water molecules?
Those water molecules might have the same residue id.

On Mon, Aug 17, 2015 at 1:42 PM, Jorge Fernandez de Cossio Diaz <
cossio at cim.sld.cu> 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 advance. Best, cossio
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