Hi Dan,
I did as you suggested, however I have a query.
I’m using the following command to look for contacts between CA on ASP 3 & C5 on Cytosine 326. However, this gives me a value greater than 1. On further atomic analysis, this is because it is also taking into account C5’. How do I only look for contacts between the C5 (NOT C5’) and CA ?
nativecontacts name sam68_25N-3CA-326C5-1 :
3.CA= :326.C5= out C5.all.res.dat reference map mapout C5-resmap.dat contactpdb Loop-NDP.pdb series seriesout C5-native.dat
#Atom Atom sam68_25N-3CA-326C5-1[nonnatmap]
5360.000 34.000 0.7883
5371.000 34.000 0.3596
34.000 5360.000 0.7883
34.000 5371.000 0.3596
where:
5360 is C5’ & 5371 is C5
more SAM68-C25-BOX.pdb|grep -v WAT|grep 5360
ATOM 5360 C5' C 326 -6.295 26.880 17.879 1.00 0.00
more SAM68-C25-BOX.pdb|grep -v WAT|grep 5371
ATOM 5371 C5 C 326 -6.351 30.781 20.616 1.00 0.00
Regards
Sid
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Dr Khushwant Sidhu
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On 16/03/2017, 12:41, "Daniel Roe" <daniel.r.roe.gmail.com> wrote:
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
> Senior Experimental Officer / I. T. Professional
>
> Department of Molecular and Cell Biology,
> 1/61 Henry Wellcome Building , University of Leicester,
> Lancaster Road,
> Leicester,
> LE1 7RH
>
> T: 0116 229 7237
> E: k.sidhu.le.ac.uk
> [cid:image001.gif.01D29E41.3290A9D0]
> Elite without being elitist
> Follow us on Twitter<https://twitter.com/uniofleicester> or visit our Facebook<http://www.facebook.com/uniofleicester> page
>
>
>
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Tue Apr 04 2017 - 02:00:02 PDT
