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

From: Mrinda Jones <>
Date: Wed, 3 Jun 2015 11:56:00 +0530

Hi Dac and Hector,

The system details are:
Force field : gaff and ff99SB
System Length : 212 residues (protein) and one Drug
Overall Protein is Neutral and Drug has -2 Net charge
Thermostat and barostat used: Langevin thermostat (NTT=3),
MC Barostat was default i.e 1, ntp=1

My question is, is this density being less than 1gg/cc justifiable in terms
of MD run. Is the run okay?

When I visualize in VMD the trajectory for the drug-protein interaction
does not any show blow off. Moreover the protein I have used is a modeled
one. The temperature, pressure, volume and Energies are showing stable
graphs as expected from a normal 80 ns run.

What can a rmsd data tell about the simulation? Is it necessary for the
rmsd to get stabilized below 3 or 4 Angstrom in case of modeled protein
runs as well as there is an non-modeled loop region towards the

M. Jones

On Wed, Jun 3, 2015 at 1:11 AM, David A Case <>

> 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.
> ...dac
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Received on Tue Jun 02 2015 - 23:30:03 PDT
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