Hi Kellon,
If you're looking to automate comparisons to the components.cif
substructures, OpenFF has some prototype code that programmatically parses
cif files and makes chemical structures [1]. With a little tweaking this
could work independently of the OpenFF stack and just use RDKit (or a more
AMBER-friendly chemistry program). I'd be happy to screenshare for an hour
or two if this is of interest to you!
[1]
https://github.com/openforcefield/openff-toolkit/blob/topology-biopolymer-refactor/openff/toolkit/utils/_cif_to_substructure_dict.py
Cheers,
Jeff
On Tue, Nov 16, 2021 at 5:02 AM Kellon Belfon <kellonbelfon.gmail.com>
wrote:
> Okay I can make the change along with the updates to the modified amino
> acids so that they are consistent with the .cif format as well. Thank you!
>
> On Tue, Nov 16, 2021, 7:49 AM David A Case <david.case.rutgers.edu> wrote:
>
> > On Tue, Nov 16, 2021, Kellon Belfon wrote:
> > >
> > >I had looked at NME and saw we were using different atom names and
> figured
> > >the capping groups in general doesn't match with the PDB but indeed ACE
> > >matches. In that case should we change NME to be consistent?
> >
> > Yes, I think we should.....dac
> >
> >
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Received on Tue Nov 16 2021 - 10:00:03 PST
