Hi,
You are including the wildcard character '=' at the end of each mask,
so :326.C5= will match both C5 and C5' atoms. Remove the '='
character.
-Dan
On Tue, Apr 4, 2017 at 4:50 AM, Sidhu, Khushwant (Dr.)
<k.sidhu.leicester.ac.uk> wrote:
> 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
>
> ------------------------------------------------------------------------------------
>
> 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
>
> Elite without being elitist
> Follow us on Twitter <https://twitter.com/uniofleicester> or visit our Facebook <http://www.facebook.com/uniofleicester> page
>
>
>
> 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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
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> https://www.lobos.nih.gov/lcb
>
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-------------------------
Daniel R. Roe
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National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
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https://www.lobos.nih.gov/lcb
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Received on Tue Apr 04 2017 - 05:30:04 PDT
