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>
app.run_mmpbsa()
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
self.prmtop))
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
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Received on Sun Mar 25 2018 - 22:30:03 PDT
