Re: [AMBER] covalently bound ligand

From: FyD <>
Date: Tue, 15 Nov 2016 08:36:17 +0100

Dear Ahsan,

> 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.

Please see R.E.D. Server Dev./PyRED at
You will be able to generate potentially any molecular fragment
starting from a whole molecule
                     all the elements of the periodic table are handled
                     you will be able to provide missing FF parameters
                     as well defining new atom types, and far more...

See tutorials:

regards, Francois

           F.-Y. Dupradeau

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Received on Tue Nov 15 2016 - 00:00:02 PST
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