Hi David,
In natural residues yes. But sometimes I have small molecules where the atom name is not unique (as output of tleap). Like for instance for ATP. This is actually the problem. Even with the mapping you referred to I would not be able to clearly identify the atoms.
Something wrong going on during the MD preparation then?
Cheers.
Peter
-----Message d'origine-----
De : David A Case [mailto:david.case.rutgers.edu]
Envoyé : mardi 19 avril 2016 15:20
À : AMBER Mailing List
Objet : Re: [AMBER] atom serials instead of residue names and atom names in nativecontacts cpptraj
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 - 08:30:04 PDT
