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.
Best£¬
Fengshi
At 2022-06-20 21:16:27, "Matthew Guberman-Pfeffer via AMBER" <amber.ambermd.org> 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?
>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.
>
>Best,
>Matthew
>
>
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Received on Thu Aug 04 2022 - 13:33:00 PDT
