Re: [AMBER] Calculating ligand contribution is failing- MMPBSA method

From: George Tzotzos <>
Date: Tue, 27 Mar 2018 12:15:05 +0200

I believe that your syntax for is wrong.

At your terminal, do -help. You’ll get an idea of the correct syntax. You can generate complex, receptor and ligand topology files with one command only.



> On 26 Mar 2018, at 07:20, varun dewaker <> wrote:
> 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
> -p ionized-3rqd-lar-hoh-n.prmtop -c complex.prmtop --strip-mask ":WAT"
> -p complex.prmtop -r receptor.prmtop -l ligand.prmtop -n ":WAT:LAR"
> than we ran the binding free energy calculation using the following command
> -O -i -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/", line 100, in <module>
> app.run_mmpbsa()
> File "/home/varun/amber17/lib/python2.7/site-packages/MMPBSA_mods/", line 218, in run_mmpbsa
>, self.stdout)
> File "/home/varun/amber17/lib/python2.7/site-packages/MMPBSA_mods/", line 82, in run
>, stdout=stdout, stderr=stderr)
> File "/home/varun/amber17/lib/python2.7/site-packages/MMPBSA_mods/", 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 Tue Mar 27 2018 - 03:30:02 PDT
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