Thank you for your suggestion sir.
________________________________
From: Elvis Martis <elvis_bcp.elvismartis.in>
Sent: Tuesday, August 6, 2019 8:51:33 PM
To: AMBER Mailing List
Subject: Re: [AMBER] error during the calculation of MMPBSA
Then you can try what Ray has suggested.
Set radiopt=0.
On Tuesday, August 6, 2019, Jeyaram R A <ra.jeyaram.vit.ac.in> wrote:
> Respected Elvis Martis sir,
>
> I am using default PBradii of mbondi2
> ________________________________
> From: Elvis Martis <elvis_bcp.elvismartis.in>
> Sent: Tuesday, August 6, 2019 7:24:02 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] error during the calculation of MMPBSA
>
> Hello,
> What default PBradii have you defined??
> Best Regards
>
>
>
> On Tue, 6 Aug 2019 at 18:37, Jeyaram R A <ra.jeyaram.vit.ac.in> wrote:
>
> > Dear Amber Users,
> >
> >
> > I did the 50ns MD simulation of protein-ligand complex
> > system by using ff14SB force field for protein and glycam force field for
> > ligand (sialic acid). From the output trjectories I am trying to
> calculate
> > the MM-PBSA binding free erergy of this complex system. During the
> > calculation i have the error as "CalcError:
> > /home/vit/Documents/amber16/bin/mmpbsa_py_energy failed with prmtop
> > comp.top!
> >
> > PB Bomb in pb_aaradi(): No radius assigned for atom 5755 O1 Oh"
> .
> > In that following I am attaching the ligand pdb file and the output of
> the
> > terminal. Help me to solve this error.
> >
> >
> >
> > MMPBSA.py -O -i mmpbsa.in -o 1.out -sp 1.prmtop -cp comp.top -rp
> prot.top
> > -lp lig.top -y md1_50.nc
> > Loading and checking parameter files for compatibility...
> > mmpbsa_py_energy found! Using
> > /home/vit/Documents/amber16/bin/mmpbsa_py_energy
> > cpptraj found! Using /home/vit/Documents/amber16/bin/cpptraj
> > Preparing trajectories for simulation...
> > 1500 frames were processed by cpptraj for use in calculation.
> >
> > Running calculations on normal system...
> >
> > Beginning PB calculations with
> > /home/vit/Documents/amber16/bin/mmpbsa_py_energy
> > calculating complex contribution...
> > File "/home/vit/Documents/amber16/bin/MMPBSA.py", line 100, in
> <module>
> > app.run_mmpbsa()
> > File
> > "/home/vit/Documents/amber16/lib/python2.7/site-packages/
> MMPBSA_mods/main.py",
> > line 218, in run_mmpbsa
> > self.calc_list.run(rank, self.stdout)
> > File
> > "/home/vit/Documents/amber16/lib/python2.7/site-packages/
> MMPBSA_mods/calculation.py",
> > line 82, in run
> > calc.run(rank, stdout=stdout, stderr=stderr)
> > File
> > "/home/vit/Documents/amber16/lib/python2.7/site-packages/
> MMPBSA_mods/calculation.py",
> > line 433, in run
> > self.prmtop) + '\n\t'.join(error_list) + '\n')
> > CalcError: /home/vit/Documents/amber16/bin/mmpbsa_py_energy failed with
> > prmtop comp.top!
> > PB Bomb in pb_aaradi(): No radius assigned for atom 5755 O1 Oh
> >
> > Exiting. All files have been retained.
> >
> >
> >
> > Thanks in advance
> > with regards
> > R. A. Jeyaram
> > Research scholar
> > Vellore Institute of Technology
> > Tamil Nadu, India.
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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>
--
Best Regards
Elvis Martis
Mumbai.
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Received on Tue Aug 06 2019 - 08:30:03 PDT
