On Wed, Oct 21, 2020, Gustaf Olsson wrote:
>I just noticed that while adding “CL” neutralised the charge just fine,
>however there are seemingly two “default” options, CL and Cl-.
Just a comment on this issue: The PDB standard for chloride ion has
both the residue name and atom name as "CL". Amber users should follow this
convention.
Back in the olden days, Amber developers (and many others in the field)
paid scant attention to standards, and decided to use names like "Cl-".
After we (tried to) update Amber to use PDB standards, it was decided
(mainly by me, I think) to allow backwards compatibility for Na+,
K+ and Cl-. This meant that old input files for these common ions would
still "work", but was probably a mistake overall -- having just one
naming scheme (the PDB one) makes more sense. People would change
things once, then not have to worry later.
If you look in $AMBERHOME/dat/leap/lib/atomic_ions.lib, you will still
see a mixture of PDB-standard names and older ones. It's a medium-sized
job to clean all this up, but it would be nice to get someone to do
this at some point.
One final potential source of confusion: Amber also uses atom *types*,
but these are internal names, and aren't required to follow any
conventions. Hence, for residue K, atom K, the atom type is "K+".
....dac
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Received on Thu Oct 22 2020 - 05:30:02 PDT
