Thank you for clarifying, after these emails the “ion” situation all makes a lot more sense to me.
Unfortunately, I opted for Cl- as it aligned easily and nicely with regards columns in the pdb files generated. For future reference, I now know better and will adapt the more appropriate option.
Thank you and best regards
// Gustaf
> On 22 Oct 2020, at 14:21, David A Case <david.case.rutgers.edu> wrote:
>
> 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 - 05:30:03 PDT
