I am trying to run a QM/MM in Amber on a protein-ligand system. I have looked for tutorials but they don't explain a few things such as how to heat your system and equilibrate it before MD.
Then there are errors in output files. I have run the questions in the list and applied the changes, but the errors still remain. I would appreciate if someone could share their experience on running these for protein-ligand systems.
Thank you.
Dear Ayesha,
If would be more helpful if you include your error massage in your question.
thanks
Dear Ayesha,
I think it is very difficult to answer your question unless you give the error message and describe your question more clearly.
Hi,
This tutorial is very helpful:
http://sf.anu.edu.au/collaborations/amber_on_fujitsu/amber-12/tutorial/amber-gaussian/index.html
As to the errors you got, I second the previous two comments. You need to specify the errors you are getting.
Ahmed
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