Dear Experts,
I am following the tutorial
https://ambermd.org/tutorials/advanced/tutorial6/index.php
In this tutorial, they describe the Asp residue, for which the VDW terms of
the hydroxyl hydrogen are fortunately set to zero.
I want to calculate the free energy difference between protonated Lys and
deprotonated Lys. However, for the hydrogens bound to nitrogen, the VDW
parameters are *not zero*. Should I explicitly modify the VDW parameters in
the deprotonated Lys prmtop file?
--
*With regards,*
*Dulal Mondal,*
*Research Scholar,*
*Department of Chemistry,*
*IIT Kharagpur, Kharagpur 721302.*
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Received on Fri Aug 29 2025 - 07:00:02 PDT
