[AMBER] mmpbsa.py to calculate binding energy between protein and a ligand when there are two ligands combined with the protein.

From: 幀 羣梱 <jewelryono.outlook.com>
Date: Mon, 11 Jul 2016 09:19:28 +0000

Dear Amber members:

     I want to calculate the binding energy between the protein and a ligand,the protein has two ligands at different binding sites.I would like to know how to write or add some commands in mmgbsa.in file.I have not seen any previous examples of this problem.My mmpbsa.in file is below.

     I wonder if anyone can help me in this regard.Looking forward to your replies.

                     mmpbsa.in input file

input file for running PB and GB
   startframe=15001, endframe=20000, interval=2,
  igb=5, saltcon=0.100,
 idecomp=2, dec_verbose=1
 nmstartframe=1, nmendframe=2500,
   nminterval=25, nmode_igb=1, nmode_istrng=0.1,
    Thank you so much!
    JH ZHU.

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Received on Mon Jul 11 2016 - 02:30:02 PDT
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