Re: [AMBER] Issue running sander

From: Clorice Reinhardt <>
Date: Wed, 25 Aug 2021 17:01:10 -0400

Hi Gabby,
This is a typical error message is from the job scheduler on the cluster,
and it says exactly what it means- it didn't find the executable for
sander. Did you load the module in your submit script? Is $AMBERHOME
defined? Most of these are quick fixes on a typical supercomputing cluster
and come with familiarity. You can find some answers on setting $AMBERHOME
from other forum posts, and your local cluster should have information on
the module system to help you find the proper module (If you didn't install
this build yourself, which i'm assuming).
Hope that's helpful,

On Wed, Aug 25, 2021 at 4:22 PM Vento, Gabby <> wrote:

> Hello everyone,
> I keep getting an error message when I try to run my script that says
> "slurmstepd: error: execve(): sander.MPI: No such file or directory". What
> does this mean and how do I fix it?
> This is the script I am trying to run:
> srun sander.MPI -O -i mini -o mini.out -p ../PREP/ -c
> ../PREP/WT_ATR_solvate.crd -r mini.rst -ref ../PREP/WT_ATR_solvate.crd
> -Gabby Vento, M.S.
> (she / her / hers)
> College of Medicine and Life Sciences
> Doctoral Student: Biomedical Sciences - Bioinformatics
> _______________________________________________
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Received on Wed Aug 25 2021 - 14:30:02 PDT
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