Hi Jonathan,
> Em 07/10/2015, à(s) 17:41, Jonathan Sheehan <jonathan.sheehan.gmail.com> escreveu:
>
> Gustavo,
>
> Thanks for the work-around. Yes, editing the .prmtop file works for
> me, too. (It produces .pdb files that don't confuse PyMOL.) But just
> to be clear, is this a (minor) bug, or am I doing something wrong?
I’d say it used to be a ’feature’ at some point, when Amber didn’t care about the atomic numbers. But it turned out to be a bug now, since old files are misleading Amber.
> For anyone else running into this problem: you can use cpptraj in
> place of ambpdb. It seems to take the .prmtop with (-1) in the
> ATOMIC_NUMBER positions for O3, and produce a .pdb file that correctly
> has O in the element column. Magic! (Maybe it keys off the mass?)
Cpptraj has other means of detecting the atom symbol, other than atomic number. In this case, it is probably determining the symbol just by looking at the first letter.
I’m glad it is working for you now!
Gustavo.
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Received on Wed Oct 07 2015 - 19:30:04 PDT
