[AMBER] Per residue free energy decomposition is not working

From: ABDUL BASIT <abdul48_sit.jnu.ac.in>
Date: Wed, 7 Apr 2021 21:12:10 +0530

Dear All

I am trying to calculate binding free energy decomposed per residue basis
using MMPBSA.py script. My input file is as follows


Input file for running PB
&general
   startframe = 5001
   endframe=10000
   verbose=1,
   interval =50
   keep_files=0
   receptor_mask= :1-147
   ligand_mask= :148
/
&pb
  indi =8
  istrng=0.150,
/

&decomp
  idecomp=1, print_res="1-148"
  dec_verbose=1,
/


The total binding free energy and sum of free energies from individual
residues are not matching if the dielectric constant is different from 1. I
am attaching here my results at dielectric constant = 8.



Sincerely

Abdul Basit
Research Fellow
School of Computational & Integrative Sciences
Jawaharlal Nehru University, New Delhi-110067
India


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Received on Wed Apr 07 2021 - 09:00:05 PDT
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