[AMBER] Help with MDCRD file for calculating binding energy

From: Ram Koganti <rkogan3.uic.edu>
Date: Fri, 7 Aug 2020 20:36:34 -0500

Hi all!

I'm new to AmberTools, and I am trying to find the binding energy of a
protein-protein conformation in a PDB file. I am following the tutorial
given in this link:
https://ambermd.org/tutorials/advanced/tutorial3/py_script/section1.htm. I
think I know how to generate the prmtop files from my PDB file. However, I
am not sure how the MDCRD input file works. Is there a MDCRD file that I
have to input along with the prmtop files? If so, does anyone know how to
generate it? If not, does the MMPBSA.py file automatically generate all of
the MDCRD files that I need?

If anyone could provide some guidance on how to do any of the above steps,
that would be greatly appreciated. Thank you so much for your help!

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Received on Fri Aug 07 2020 - 19:00:02 PDT
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