AMBER Archive (2006)

Subject: Re: AMBER: grid output

From: Sergey Samsonov (sergeys_at_biotec.tu-dresden.de)
Date: Tue Nov 07 2006 - 10:46:07 CST

Dear Mr. Cheatham,

Thomas Cheatham wrote:
>
>> 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.
>
Actually I meant something different (sorry for not very clear way of
putting it before).
Under moment I meant the value of the isosurface one observes when one
analyzes .xplor
file (number of hits). It is possible to compare, for example, the
isosurface values when
the "grid volumes" are of size of oxygen atom or water molecule or
something else. So when they
are visually 'appearing' after change of hits threshold one can compare
the different values for
different points in the space. Have I understand that correctly or in
the article of yours (1996)
you used some scripts to analyze the .xplor output without visualizing
the output in advance?

Thank you very much for the help!
> 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.
>
Yes, in my case I had done rms centered on the residues of interest in
advance.

Sergey
> --tom
>
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