Re: [AMBER] {SPAM?} 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.

From: Matthew Guberman-Pfeffer via AMBER <>
Date: Mon, 20 Jun 2022 09:16:27 -0400

Hello Fengshi,

> After using amber16 for classical dynamics simulation, I directly used the generated prmtop file and rst file for QM/MM MD simulation with gaussian09.

I imagine you are using the QM/MM interface to generate the files for Gaussian?
I’ve done that for heme systems as well and I’ve never seen this issue (just checked my files and they all have Fe).

Are you editing gau_job.inp with a script? Maybe when you are splitting the fields on the line the script is dropping the second character of the atomic symbol?

An easy fix, regardless of cause, would just be to do something like: sed -I ’s|F |Fe |g’ gau_jog.inp on the command line. But just make sure no other “F” gets changed (pad the expression with enough spaces to be unique). Really, though, this should not be needed if you figure out the original issue.


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Received on Thu Aug 04 2022 - 13:32:25 PDT
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