Re: [AMBER] Density for a protein ligand complex run

From: David A Case <>
Date: Tue, 2 Jun 2015 15:41:53 -0400

On Tue, Jun 02, 2015, Mrinda Jones wrote:
> And after simulation run for 80 ns, the summary.DENSITY file shows an
> average density of 0.98 which is stable but less than 1 gm/cc.

I agree that this seems a little low. But without knowing what force
field you used, how big the protein is, what its overall charge is, what
thermostat and barostat you used, and so on, it's hard to be of much help.

Plus, I almost never use TIP3P water; maybe people on the list can report
on what sorts of densities they typically see for a protein in a 12 Ang buffer
box of TIP3P water.


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Received on Tue Jun 02 2015 - 13:00:02 PDT
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