[Dock-fans] Amber Dock -protein charge

Scott Brozell sbrozell at scripps.edu
Thu Jan 22 14:58:49 PST 2009


Hi,

On Wed, 21 Jan 2009, Rima Chaudhuri wrote:

> I am re-scoring some ligands using Amber-dock 6.2. While generating
> the complex and receptor input files(.inpcrd and .prmtop), the log
> file reports a warning of the protein having  charge "WARNING: The
> unperturbed charge of the unit: 10.999900 is not zero.".
> I needed clarification on some issues. When running a MD simulation
> using Amber, we always neutralize the whole system. Since, amber-dock
> essentially minimizes and equilibrates, does the system here not have
> to be neutral also? I understand even if the protein is neutralized
> using antechamber, but while trying to dock say 1000 ligands with some
> charged ones, the system will revert back to being not-neutral for the
> complex. So, what is the suggestion for such cases?

It is prudent to check the warnings.
The degree of concern over this warning depends on its cause.
It could be serious if it is due to inadequate receptor preparation,
eg, incorrect protonation states, unintended counterions, etc.
It could also be innocuous.

Amber Score is similar to normal Amber MD.
Note that Amber Score uses implicit solvation; in normal Amber GB MD
charge neutralization with explicit ions is usually not performed.
It is possible to add automatic neutralization to the Amber Score preparation
scripts so that each complex is neutralized.  This may be useful for special
situations, but for the typical protein-ligand complex neutralization
has not been performed and has not been viewed as necessary.

Scott



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