[AMBER] GIST hydration analysis of big interface

From: Sergey Samsonov <sergeys.biotec.tu-dresden.de>
Date: Fri, 7 Oct 2016 16:22:53 +0200

Dear AMBERs,

I'm trying to calculate hydration properties of a relatively big
interface between two macromolecules. Because the interface that
interests me consists of quite an extended H-bonding network (made up of
direct and water-mediated H-bonds) I'd like to apply GIST calculations
in the box containing the whole interface and, then, to get hydration
properties around the residues establishing this H-bonding network. To
do this I can use GistPP in the way it is shown in the tutorial.
However, I face a technical problem, which was previously already
partially discussed in the Mailing List: when I run GIST in a big box, I
get an error probably due to the memory shortage:
  1: [gist doorder doeij gridcntr 62 69 60 griddim 60 60 60 gridspacn
0.5 out Region3/gist.out]
     GIST number of voxels: 216000, voxel volume: 0.125000 A^3
     GIST grid origin: 47.000 54.000 45.000
./run_gist3.com: line 1: 12480 Killed cpptraj
../../top.top < gist3.ptraj

The same script starts to work without any problem when I decrease the
box sizes to 45 45 45 and still does not work if I just take
significantly less frames (I even tried with just one frame to check if
this could work) from the trajectory for my analysis.

I guess an intuitive way to overcome this obstacle is to split the
interface into several smaller boxes that do not yield problems for GIST
calculations, to cary out calculations for them and then to unite them.
The technical question is if it is possible to take two overlapping
boxes and unite them into one using GistPP?

Maybe I'm doing something wrong with my trajectory: prior to the
analysis I image the trajectory using a script containing centering and
rms to the the solute, and imaging with 'image center familiar' command.
Could this be a source of the error in following GIST calculations?

Thank you very much in advance and cheers,


Sergey A. Samsonov
Postdoctoral researcher
Structural Bioinformatics
Biotechnology Center
Tatzberg 47-51
01307 Dresden, Germany
Tel: (+49) 351 463 400 83
Fax:   (+49) 351 463 402 87
E-mail: sergey.samsonov.biotec.tu-dresden.de
Webpage: www.biotec.tu-dresden.de
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Received on Fri Oct 07 2016 - 07:30:02 PDT
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