On Fri, Feb 09, 2018, Ruth Helena Tichauer wrote:
>
> When trying QM/MM with an internal QM method, it appears that the atom type of three oxygens from my ligand are unknown. Here is the error message:
>
> QMMM: Atom number: 107 has atomic number -1
>
> > source oldff/leaprc.ff99bsc0
> > loadoff mga.lib
> Loading library: ./mga.lib
> Loading: MGA
> > loadamberprep gtp.prep
> Loading Prep file: ./gtp.prep
> (UNKNOWN ATOM TYPE: O3)
> (UNKNOWN ATOM TYPE: O3)
> (UNKNOWN ATOM TYPE: O3)
I'm unable to reproduce these "UNKNOWN ATOM TYPE" messages. What version of
AmberTools are you using?
Try loading the following in leap, at the beginning:
addAtomTypes{
{ "O3" "O" "sp2" }
}
That should force leap to recognize that atom type O3 is in oxygen.
...hope this helps....dac
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Received on Mon Feb 12 2018 - 05:00:02 PST
