[AMBER] Free energy calculation of complex with covalent bond

From: SUBHASMITA MAHAPATRA MAHAPATRA via AMBER <amber.ambermd.org>
Date: Tue, 20 Aug 2024 15:41:02 +0530

Hi,

I want to calculate free energy between a ligand and its receptor protein.
but, the ligand is forming a covalent bond with the 46th serine residue of
the receptor. While preparing .prmtop files for MMPBSA, the ligand file
contains the ligand along with 46th serine and a void formation happens in
the 46th position in the receptor file. I would like to know how to take
care of this problem.

Thank you

-- 
*Yours Sincerely*
*Subhasmita Mahapatra*
*Ph.D. Scholar (PMRF)*
*Computational Biophysics Group*
*Department of Biosciences and Biomedical Engineering*
*Indian Institute of Technology, Indore*
*Madhya Pradesh, India (453552)*
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Received on Tue Aug 20 2024 - 03:30:02 PDT