On 19.06.2013 19:03, Daniel Roe wrote:
> Hello All,
>
> I would like to announce update 10 for AmberTools 13, which contains
> several enhancements to and bug fixes for CPPTRAJ. This updates
> CPPTRAJ to version 13.10 and includes the following:
>
> 1) Adds the 'mindist' action. This will calculate the minimum distance
> between atoms in two non-overlapping masks. Usage:
> mindist [<name>] <mask1> <mask2> [out <filename>] [noimage]
> Imaging is performed by default when box information is present unless
> the 'noimage' keyword is given.
>
Thanks, that was fast and thanks for your work on cpptraj in general :-)
I've been working on this today myself and then found it pretty
convenient to also calculate the average minimal distance for all atoms
in mask 1 from any atom in mask 2. Meaning:
For each atom in mask 1 calculate the distance to all atoms in mask 2
and select the minimum, yielding one minimal distance value per atom in
mask 1. Finally, average over these minimal values.
Considering a system comprised of receptor and ligand, this provides an
intuitive measure of how far both molecules are separated from each
other on average. I am working with protein-sugar interaction, at least
there this measure can be quite meaningful. The sugar could be attached
to the protein with one end (simple mindist would be small), but the
rest of it might point away in the solvent (the averaged distance
described above would be large).
Cheers,
Jan-Philip
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Received on Wed Jun 19 2013 - 11:30:03 PDT
