Ahh both of you are right. Thank you for clearing that up for me .David Case
<david.case.rutgers.edu>
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?
I guess moving forward the burden is on other softwares to update their
standard to the components.cif file.
On Mon, Nov 15, 2021, 9:21 PM Eric Pettersen <pett.cgl.ucsf.edu> wrote:
> e.g. in entry 1e10, the names are H1, H2, H3.
>
> --Eric
>
> > On Nov 15, 2021, at 6:17 PM, David A Case <david.case.rutgers.edu>
> wrote:
> >
> > On Mon, Nov 15, 2021, Kellon Belfon wrote:
> >>
> >> I noticed that there was a change to the Atom name in the capping group
> ACE
> >> a couple years back. The changes were HH31, HH32, HH33 to H1, H2, H3.
> >>
> >> These new atom names do not appear to be in line with standard PDB atom
> >> names for ACE. Is there a reason for this change? And does anyone
> oppose to
> >> or feel strongly against changing it back?
> >
> > I made the changes described above, but to me they appear to be the
> correct
> > changes. I just downloaded the latest components.cif file from here:
> >
> > https://www.wwpdb.org/data/ccd
> >
> > and hydrogen names are indeed H1,H2,H3. Why do you think that these "are
> > not in line with standard PDB atom names for ACE"? The components.cif
> file
> > should be the authoritative source.
> >
> > ...thx....dac
> >
> >
> > _______________________________________________
> > AMBER-Developers mailing list
> > AMBER-Developers.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber-developers
>
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
Received on Mon Nov 15 2021 - 23:00:02 PST
