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

From: David A Case <>
Date: Wed, 3 Jun 2015 09:14:39 -0400

On Wed, Jun 03, 2015, Mrinda Jones wrote:
> 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?

Based on what you report, I would not view a density of 0.98 as a red flag.

> 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
> protein-tail.

It is not clear what reference structure you are using for the RMSD

In cases like this, it is often very helpful to compute the backbone RMSD
leaving out loops and tails. But there is no magic number: visually comparing
the starting and ending structures will tell you whether the overall fold has
changed or not. In a 200 residue protein, you can easily get RMSD values of 3
or 4 Ang (espeically if you are including loops and tails) when the overall
fold has changed very little.


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Received on Wed Jun 03 2015 - 06:30:03 PDT
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