Re: [AMBER] processing trajectories subjected to GIST analysis

From: Daniel Roe <>
Date: Tue, 30 Apr 2019 09:58:42 -0400


On Thu, Apr 25, 2019 at 12:49 PM Alfredo Quevedo
<> wrote:
> I am trying to apply a GIST analysis to an explicit solvent trajectory
> containing a protein. My question is wheter an autoimage action is
> required to reconstruct the solvent box prior to the GIST analysis? If

Since GIST is a grid-based method, the results depend upon how the
solute/solvent are oriented with respect to the grid. In general, you
should autoimage w.r.t. the region of interest (so e.g. if you're
focusing on a specific binding site, you should 'anchor' on that site)
then rms-fit the trajectory so you remove any global rotation and
translation. So for example you could autoimage to the origin, then
put your gist 'gridcntr' at 0 0 0.

> this is done, the behavior of explicit water molecules respect to their
> translation and orientation is lost, am I correct? Also, applying SHAKE

The only property that imaging direcly impacts is diffusion - but
since this is a grid based method all that matters is that the grid is
stable w.r.t to your reference frame (usually the solute), which is
what the rms fit is for.

> to the obtention of these trajectories is not correct?

SHAKE is in fact required for rigid water models to perform properly,
so you need it on.

Hope this helps,


> Thanks in advance for the info,
> best regards
> Alfredo Quevedo
> --
> *********************************************************
> Prof. Dr. Mario Alfredo Quevedo.-
> Laboratorio de Química Medicinal.-
> Dpto. de Ciencias Farmacéuticas -
> Fac. de Ciencias Químicas-
> Universidad Nacional Córdoba.-
> 5000 Córdoba, Argentina
> TE: +54 351 5353865 Int: 53355
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Received on Tue Apr 30 2019 - 07:00:02 PDT
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