On Sun, 2015-08-02 at 18:47 -0400, Jose Borreguero wrote:
> Dear AMBER users,
>
> >From the results I'm getting it would seem that the "contacts" command of
> cpptraj does not implement imaging. Can anyone please confirm this?
>
> My input script evaluating contact between atom "C" of residues 4124 and
> 1150:
>
> trajin equil.dcd 5001 5001
> 1
>
> distance :4124.C :1150.C out
> junk.dat
>
> contacts (:4124,1150)&.C distance 7.0 out
> junk2.dat
> go
>
> quit
>
> I execute as: cpptraj -p pdbfile -i inputScriptFile
>
> The contents of junk.dat:
> #Frame Dis_00000
> 1 6.0495
>
> The contents of junk2.dat:
> #time Contacts native Contacts
> 1.00 0 0
>
> There's a discrepance here, since the distance of 6.0495 is well below my
> 7. 0 cutoff. I should be getting one contact
As your observations here note, the "contacts" action does not account
for imaging (you can verify this in the source code). However, the
"nativecontacts" command, which probably does what you want it do,
*does* account for imaging (unless you explicitly request that it not
via the `noimage` keyword).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Aug 03 2015 - 06:30:02 PDT
