Hi Daniel,
Thanks for your reply. What you suggested is what I'm already doing right now, but I wondered if there was something already integrated but yet not documented or so. I'll patiently wait and use the less elegant scripting way the time being ;)
Cheers.
Peter
-----Message d'origine-----
De : Daniel Roe [mailto:daniel.r.roe.gmail.com]
Envoyé : lundi 29 février 2016 16:32
À : AMBER Mailing List
Objet : Re: [AMBER] Bounds command with GIst
Hi,
Currently the 'gist' Action in cpptraj has not been fully integrated into the DataSet/DataFile framework; although there are plans to do this, it may not happen soon.
However, you could do this inside of a single script via two cpptraj runs; just parse the output of 'bounds'. For example, if you wanted to get the bounds of a solute which comprises residues 1 to 13 along with grid parameters appropriate for 0.5 Ang spacing:
cpptraj <<EOF
parm myparm.parm7
trajin mytraj.nc
bounds :1-13 dx 0.5 name MyGrid out bounds.dat EOF
The contents of bounds.dat might be something like:
11.283378 < X < 26.885846 Center= 19.084612 Bins=33
11.268203 < Y < 32.083336 Center= 21.675769 Bins=43
9.850358 < Z < 26.139364 Center= 17.994861 Bins=34
Parse this using your favorite scripting tool (I would probably use
'awk') to get the arguments for GIST 'gridcntr' and 'griddim'
keywords.
Hope this helps, and thanks for bringing the issue up.
-Dan
On Mon, Feb 29, 2016 at 3:35 AM, <peter.schmidtke.discngine.servier.com> wrote:
> Hi all,
>
> I'd like to know if there are plans or are already ways to use the bounds calculated bounding box of a putative grid for Gist calculations in cpptraj.
>
> Couldn't find any documentation on that I would like to avoid specifying the bounding box by hand inside the ptraj script.
>
> Thanks in advance for your reply.
>
> Peter
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Mon Feb 29 2016 - 23:30:04 PST
