On Fri, Jul 07, 2023, Riran via AMBER wrote:
>I tried what you suggested, but it didn't work out. I tried MN , Mn2+, Mn,
>but none of them worked.
Use (for example) ambpdb to create a pdb file for your system, and see what
the residue names are in your particular system. The PDB (and Amber)
standard is to use MN as the residue name for manganese.
Aside: you use of Na+ and Cl- is also non-standard: the correct names are NA
and CL. I'm not sure you you prepared the system to get these names. (This
is a curse of backwards-compatibilty: in the previous millenium, after the
deluge but before the internet, Amber developers started using Na+ and Cl-.
We somewhat foolishly tried to keep this as an alternative (for just these
two ions plus K+), but that inevitably leads to confusion.)
....dac
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Received on Fri Jul 07 2023 - 09:00:06 PDT
