Hi,
On Thu, Mar 16, 2017 at 6:36 AM, Sidhu, Khushwant (Dr.)
<k.sidhu.leicester.ac.uk> wrote:
>
> distance C319-U346-ALL-LYS214-NZ :319-346.* :214.NZ out C319-346-ALL_LYS214-NZ.agr
>
> This produces one plot with one distance graph:
> Is this the minimum distance ?
> Can I show all distances (would produce hundreds of plots ?)
This will plot the distance of the center of mass of residues 319-346
to atom NZ of residue 214 (see the Amber16 manual, '29.9.25
distance').
Sounds like what you really may want is the 'nativecontacts' command
with 'mindist' for the minimum distance and 'series seriesout <file>'
to plot all distances. Note that to track non-native contacts (those
not present in your reference frame) and plot their distances you will
need to use the GitHub version of cpptraj
(
https://github.com/Amber-MD/cpptraj) and the new keywords
'savenonnative seriesnnout <file>'.
Hope this helps,
-Dan
>
> regards
>
> ------------------------------------------------------------------------------------
>
> Dr Khushwant Sidhu
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>
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-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
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Received on Thu Mar 16 2017 - 06:00:02 PDT
