[AMBER] Query about extremely large positive ΔG for protein–protein binding free energy calculation

From: Jessica Baa via AMBER <amber.ambermd.org>
Date: Tue, 7 Jul 2026 18:24:31 +0530

Dear Amber community,

While trying to compute the binding free energy of a protein complex (2700
amino acids) with another protein (550 amino acids), I am getting highly
positive delta G (~10^16 kcal/mol)

The parameters used are as follows: istring=0.15, inp=2, radiopt=0,
prbrad=1.4.

Is MMPBSA tool in AMBER capable of revealing the protein-protein binding
free energy for large complexes. If so, k let me know what might be
possibly wrong with my inputs.

I will be obliged for any leads in this regard, t you in advance.

Best regards,
Jessica

-- 
Jessica Baa
Research Scholar
Department of Biotechnology
Indian Institute of Technology, Hyderabad, Kandi, Sangareddy, Telengana
502285,India.
-- 
Disclaimer:- This footer text is to convey that this email is sent by one 
of the users of IITH. So, do not mark it as SPAM.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

Received on Tue Jul 07 2026 - 06:00:02 PDT