Re: [AMBER] covalently bound ligand

From: David A Case <>
Date: Mon, 14 Nov 2016 21:08:18 -0500

On Mon, Nov 14, 2016, Ahsan Mohd wrote:

> I have a system in which protein in covalently bound to the
> boron containing ligand with boron atom. I am confused how to proceed with
> this system.
> I have basic doubt that if I follow the normal protocol and use antechamber
> for ligand I will gonna miss the covalent bond between ligand and protein.

You are correct to have doubts. First, antechamber doesn't handle any
systems with boron. Second, antechamber won't help much for covalently
bound ligands.

There are a variety of ways to handle covalently bound ligands, but none of
the them are very straightforward, in my view. One idea is to treat the amino
acid + ligand as a modified amino acid. You'll still have to deal with the
boron problem. Expect to learn a lot about how force fields are developed,
and to carry out a number of quantum chemical calculations to characterize
your system.

...good luck....dac

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Received on Mon Nov 14 2016 - 18:30:03 PST
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