[AMBER] Error in MMPBSA

From: Saugata Hazra <saugata.iitk.gmail.com>
Date: Wed, 6 Mar 2013 15:30:00 -0500

Hi all,

I'm calculating the binding energy of a protein-ligand interaction which
contains Protein, metal and ATP.
According to your help I have put the metal with the protein and ATP was
treated as a ligand.

After that when I was trying to run, I got the following error message.

*Beginning PB calculations with /home/saugata/amber12/bin/**mmpbsa_py_energy
  calculating complex contribution...
CalcError: /home/saugata/amber12/bin/**mmpbsa_py_energy failed with prmtop
ba2291_atp_mg_vac.prmtop!
    PB Bomb in pb_aaradi(): No radius assigned for atom 2369 O1G O3

Exiting. All files have been retained.*

After that, I have followed this link
http://archive.ambermd.org/201208/0074.html and added inp=1, radiopt=0 into
the mmpbsa.in (attached with this mail)
But I'm still getting the same error message.
Please let me know if you could provide any help.




-- 
*
*
Dr. Saugata Hazra



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Received on Wed Mar 06 2013 - 13:00:03 PST
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