Re: [AMBER] Cannot minimize structure with sander

From: David A Case <>
Date: Fri, 18 Dec 2020 14:08:30 -0500

On Fri, Dec 18, 2020, George Yacu wrote:
>I am trying to run minimization with sander per the instructions in
>Tutorial 5.1 (Simple Simulation of Alanine Dipeptide). The command
>outputs the three files (min.out, min.ncrst, and min.mdinfo), but when
>I inspect the results section of min.out, it appears that the following
>error occurred:
>NetCDF error: Permission denied
>write_nc_restart(): Could not open restart

It looks like you are running in a folder where you don't have write
permissions. You can check this by running a command like "touch abc",
and see if that gives an error. You'll have to either change the folder
permissions, or move to a directory where you have such permissions.

....good luck...dac

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Received on Fri Dec 18 2020 - 11:30:02 PST
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