On Thu, Apr 11, 2024, Priyasha Majee via AMBER wrote:
>
>I want to run a 2 stage and heating minimization on Sander. I have
>MT2.prmtop and MT2.inpcrd files in the working directory as my
>parameter and coordinate files. I have a .sh file 'job. sh' which I
>have created to run stepwise jobs. When I submit .sh file, I get error
>message.
When you have errors, go back to running one command at a time. This makes
it far easier to figure how where the error is occuring.
>Error: Could not determine format of topology MT2.prmtop
I'm guessing(?) that this error came from the first "ambpdb" command, but
it's hard to be sure. Look carefully at min1.out (from the first sander
command.) Is there any indication of an error at this step?
What is the result of "head MT2.prmtop"? Does this look like a prmtop file?
>Error opening unit 30: File "min1.rst7" is missing or unreadable
This also suggests that the error is in the first sander run. Look
carefully at the min1.out file.
...good luck...dac
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Received on Fri Apr 12 2024 - 12:00:02 PDT
