Parameterizing ligands with protein

From: Lakshmi Dharmarajan (
Date: Tue May 01 2007 - 00:17:37 CDT


I want to do MD simulations on my protein with the ligand i.e.
Phosphoenolpyruvate bound to it. Can anyone tell me how to parameterize ligands
in NAMD? Is there any tutorial which can help me? I looked for help from the
tutorials on the website but couldn't find any of relevance to my problem.

Thanks a lot,

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