On Wed, Mar 25, 2020, Thomas Cheatham III wrote:
>
>>
>> Checking Unit.
>> FATAL: Atom .R<K 37>.A<K+ 2> does not have a type.
>> FATAL: Atom .R<K 38>.A<K+ 2> does not have a type.
>
>The residue name is K which is not consistent with the libraries (assuming
>you did load up some ion parameters) so if ion is in the PDB file, change
>the residue name to K+.
No,no,no....sorry to disagree with our nucleic acid expert here, but you
are better off following the wwPDB standard: both the residue name and
the atom name should be "K". This is the way it is in actual files you
would get from www.rcsb.org.
Way back in the twentieth century, force field developers (which
includes me) didn't so care much about standards, and just decided on our
own what names we should give to things like ions. So "K+" became
ingrained in people's files.
In an attempt to follow standard nomenclature, and yet still not break
too many existing scripts, Amber has made K, NA and CL special cases,
allowing users to also use the old names of K+, Na+ and Cl- (for both residue
and atom). So, Tom's suggestion *will* work: set both the residue and
atom name to "K+". But that's only for Amber: other programs are likely
to be more strict about nomenclature. The better solution is to make
both atom and residue name "K".
....dac
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Received on Wed Mar 25 2020 - 19:00:03 PDT
