AMBER Archive (2006)

Subject: Re: AMBER: grid output

From: Thomas Cheatham (tec3_at_utah.edu)
Date: Tue Nov 07 2006 - 10:25:39 CST

> Thank you very much for the help and the reference! Now it's more clear how one
> can interpret the results from grid command.
>
> If I correctly understood from the article, the moment when 'the density is
> seen' is quite arbitrary
> but since one compares different site of the same simulation (or the
> equivalent simulations) what one
> should care is just relative values.

If by "moment" you refer to time, then yes, you cannot make information
about the time scale of the density, for example 2x bulk water density
could mean that the site is occupied at 4x water density for half the
simulation and 0x the other half. For time information, I use the hbond
command.

Also, comparing hydration sites is relative and care has to be taken to
understand the mobility of the structure. Prior to calling "grid" the
solute needs to be put into a common reference frame (for example by RMS
fitting to the first frame the "region of interest"). Outside the region
of interest, motion can smear the occupancy on the grid. For example, if
you imaging a DNA duplex where you fit on the central base pair, as you
move further out from the center of the duplex, the density will
necessarily drop off on the grid due to motion (but this doesn't mean
there is not specific hydration). In some sense, to compare different
sites you will want to fit separately to each site and build a separate
grid for each site.

--tom

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