On Tue, Apr 19, 2016, peter.schmidtke.discngine.servier.com wrote:
>
> I am trying to use the nativecontacts command available in
> cpptraj. Results are pretty nice. However, I'm working on small molecule
> protein complexes. Describing contacts using the residue number and atom
> name is thus very cumbersome for me. Actually :169.O2 could represent
> whatever oxygen on a triphosphate of an ATP molecule, just to give an
> example.
I'm confused by your example. Atoms names within a residue must be unique:
there can only be one O2 atom in residue 169. So I'm not clear what you mean
by the phrase "whatever oxygen".
A pdb file (as created by ambpdb or by LEaP) shows a mapping between atom
numbers and residue-number/atom-name pairs. So maybe you could use that to
process your output to use atom numbers rather than constructs like
":169.O2".
....dac
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Received on Tue Apr 19 2016 - 06:30:03 PDT
