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: ʱ via AMBER <>
Date: Wed, 22 Jun 2022 10:39:28 +0800 (CST)

Holle Matthew

Thank you for your help.

After carefully checking the prmtop file, I found that the atomic number in the prmtop file is already wrong. I guess this may be an error in running tleap or in the system itself.


At 2022-06-20 21:16:27, "Matthew Guberman-Pfeffer via AMBER" <> wrote:
>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?
>Ive done that for heme systems as well and Ive 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.
>AMBER mailing list
AMBER mailing list
Received on Thu Aug 04 2022 - 13:33:00 PDT
Custom Search