Hi,
On Mon, Feb 15, 2016 at 9:42 AM, Michael Shokhen
<michael.shokhen.biu.ac.il> wrote:
> center :1-508 mass origin
> image origin center familiar
> average av_md3-8.pdb PDB
Note that you are only removing overall translational motion from your
average structure via the 'center' command; rotational motion will
still be present in the average. You may want to RMS best-fit to e.g.
the first structure to remove this as well (unless you want rotational
motion present for some reason). You also may want to try 'autoimage'
instead of 'center'/'image'.
> My question is: How to modify the cpptraj script in order to collect
> for the averaging only that MD frames
>
> where the interatomic distance:
>
>
> distance R5_E89 :5.67 :89.1503
>
> belongs to the interval from 3 to 5 A?
You can use either the 'filter' command if you want to process only
frames matching certain criteria with subsequent actions, or the
'outtraj' command with 'maxmin' keyword(s) if you only want to extract
said frames. For example, if you only wanted to run the 'hbond'
command on frames matching your specific criteria you could do
something like:
distance R5_E89 :5.67 :89.1503
filter R5_E89 min 3 max 5
hbond <hbond args>
If you just want to extract frames with 'outtraj':
distance R5_E89 :5.67 :89.1503
outtraj Frames_R5_E89_3_5.nc maxmin R5_E89 min 3 max 5
Hope this helps,
-Dan
>
>
> Many thanks,
>
> Michael
>
>
>
> *****************************
> Michael Shokhen, PhD
> Associate Professor
> Department of Chemistry
> Bar Ilan University,
> Ramat Gan, 52900
> Israel
> email: shokhen.mail.biu.ac.il<https://webmail.biu.ac.il/owa/redir.aspx?C=a160ef9b9a6b4d06992402715d3ee465&URL=mailto%3ashokhen%40mail.biu.ac.il>
> _______________________________________________
> AMBER mailing list
> 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)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Feb 15 2016 - 09:00:09 PST
