[gmx-users] what is the best?

Cesar Lopez inmuno_cl at yahoo.com
Thu Nov 18 03:18:54 CET 2004

I have a question about ions. I don't know what is better. I want to run a DM simulation with a Hydrolase wich has a Zn+ in the active site. actually I have built the topology file and when I try to run mdrun in MD, there is a problem about pbc: The software cant fix it, so I think is because I haven't determined about the group of the Zn, by the way, when I built the topology I used the all protein (protein+Zn) and I have never use the " ions.itp".
Could anybody give me the answer?
Thank you very much

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