Re: [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: 冯时 via AMBER <amber.ambermd.org>
Date: Wed, 22 Jun 2022 10:51:41 +0800 (CST)

Holle David,

Thank you for your help. I will try to rebuild the tleap and generate a new prmtop file according to the method you said.

Best,
Fengshi

At 2022-06-22 01:41:39, "David Poole via AMBER" <amber.ambermd.org> wrote:
>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 - 13:33:02 PDT