Re: Parameterizing ligands with protein

From: Mark Abraham (
Date: Tue May 01 2007 - 00:26:08 CDT

Lakshmi Dharmarajan wrote:
> Hi,
> 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.

This is a non-trivial topic. You don't "parameterize ligands in NAMD"
you develop an extension for a force field to use in NAMD. As such you
need to follow a procedure that is consistent with the way the force
field was designed, unless you like expensive random number generators.
There used to be a tutorial that touched on this topic - I did one at a
NAMD workshop in 2004... look closely.


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