[gmx-users] Missing charges in a .gro file

Elie M elie.moujaes at hotmail.co.uk
Mon Sep 24 06:56:14 CEST 2012

Dear all,
I have created a .GRO file from a PDB file  for a polymer. However in the PDB I have positive and negative charges of some ions where as in the produced GRO file these disappear. Are those charged atoms taken into account in the gro file as I will be doing a MD simulation of such polymers with nanotubes later and I dont want to work with the wrong GRO file....if the answer is no, how do I include them?  Thanks

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