[AMBER] Calculating ligand contribution is failing- MMPBSA method

From: varun dewaker <varun_dewaker1986.yahoo.com>
Date: Mon, 26 Mar 2018 05:20:24 +0000 (UTC)

Dear Amber user community

I am new amber. I completed my molecular dynamics of protein and liagand complex using NAMD.
After running MD I am intereasted in calculating the binding free energy.
so we have searched and came to know ambers MM/GBPSA method. We converted our psf and pdb files into amber compatible file using the chamber program under parmed. The terminal shows following warning

ParameterWarning: Atom type HA1 not present in AtomType list
ParameterWarning: Replacing bond ('CG2O7', 'OG2D5'), <BondType; k=986.000, req=1.160> with <BondType; k=986.000, req=1.170>
ParameterWarning: Replacing bond ('CG331', 'NG2S3'), <BondType; k=261.000, req=1.490> with <BondType; k=266.000, req=1.460>

after that we saved the prmtop and inpcrd using the outparm command.

Then  seperation of complex, receptor and ligand is done through these commands

ante-MMPBSA.py -p ionized-3rqd-lar-hoh-n.prmtop -c complex.prmtop --strip-mask ":WAT"

ante-MMPBSA.py -p complex.prmtop  -r receptor.prmtop  -l ligand.prmtop -n ":WAT:LAR"

 than we ran the binding free energy calculation using the following command

MMPBSA.py -O -i mmpbsa.in -sp ionized-3rqd-lar-hoh-n.prmtop -cp complex.prmtop -rp receptor.prmtop -lp ligand.prmtop -y ionized-3rqd-lar-hoh-eq-n-100stride.dcd
after that

Running calculations on normal system...

Beginning GB calculations with /home/varun/amber17/bin/sander
  calculating complex contribution...
  calculating receptor contribution...
  calculating ligand contribution...
  File "/home/varun/amber17/bin/MMPBSA.py", line 100, in <module>
  File "/home/varun/amber17/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa
    self.calc_list.run(rank, self.stdout)
  File "/home/varun/amber17/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 82, in run
    calc.run(rank, stdout=stdout, stderr=stderr)
  File "/home/varun/amber17/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 478, in run

it fails on ligand contribution, so kindly help to solve this issue, so we can further
 move. help is greatly appreciated.

Regards,Varun Kumar DewakerResearch FellowQSAR & Molecular Modelling LabMPC Division (CSN-202)CSIR- Central Drug Research InstituteLucknow - 226031 (U.P), IndiaMob:+918860194990
AMBER mailing list
Received on Sun Mar 25 2018 - 22:30:03 PDT
Custom Search