Hi
But in the amber manual it says igb=2.
Can you let me know why have you used igb=5?
with regards,
AT
________________________________
From: 幀 羣梱 <jewelryono.outlook.com>
Sent: Sunday, July 10, 2016 10:19:28 PM
To: amber.ambermd.org
Subject: [AMBER] mmpbsa.py to calculate binding energy between protein and a ligand when there are two ligands combined with the protein.
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.
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mmpbsa.in input file
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input file for running PB and GB
&general
startframe=15001, endframe=20000, interval=2,
/
&gb
igb=5, saltcon=0.100,
/
&pb
istrng=0.100,
/
&decomp
idecomp=2, dec_verbose=1
/
&nmode
nmstartframe=1, nmendframe=2500,
nminterval=25, nmode_igb=1, nmode_istrng=0.1,
/
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Thank you so much!
JH ZHU.
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Received on Mon Jul 11 2016 - 09:00:03 PDT
