[AMBER] In the QM/MM MD with g09, the Fe which in the QM region, is written as F (and the atomic number is written as 9) in gau_job.log and gau_job.Inp.

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From: David Poole via AMBER <amber.ambermd.org>
Date: Mon, 20 Jun 2022 21:16:40 +0200

Hello Fengshi,

I also experienced the same issue and it was because the pdb file was off
by a single character (as Matthew G-P notes). Another fix is to set the
element of the atom in tleap when you are making your prmtop file (i.e.
using the command "set model.RES.Fe1 element Fe") . This works if the pdb
reading is finicky with automation, for instance when using obabel to make
your pdb files, or input files from crystallographic data.

Kindly,
David
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Received on Thu Aug 04 2022 - 13:32:50 PDT