On Tue, Apr 19, 2016 at 9:23 AM, <peter.schmidtke.discngine.servier.com> wrote:
> 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?
To ensure LEaP executes correctly you usually need to make sure that
atoms in each residue have unique names. The reason is that LEaP
constructs units via residue templates (your 'lib' files), and
performs matching based on atom name. This is why you can have trouble
with LEaP when loading PDB files with non-standard atom names (O1P vs
OP1 etc). I'm surprised LEaP didn't give you any warnings to this
effect.
Cpptraj assumes that all atoms have unique names. If you want a
different output format unfortunately you'll have to edit the source
code. Changing the output format is a feature I can think of adding in
the future.
-Dan
>
> 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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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
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Received on Tue Apr 19 2016 - 09:30:02 PDT
