Use parmed and delete the addition water molecule (strip :WAT)
Best Regards
On Wed, 7 Aug 2019 at 11:06, Jeyaram R A <ra.jeyaram.vit.ac.in> wrote:
> Respected prof. Elvis sir and Ray sir,
>
>
>
> Now the MM-PBSA calculation is working well. Thank you very
> much for your valuable suggestions. Unfortunately I missed my original
> input file (pdb file for protein-ligand complex) but I have prmtop (42215
> atoms) and crd files. So I loaded these prmtop and crd files in VMD
> software and I get back the input file from VMD. Once again I generate the
> prmtop and crd file. Now the prmtop file contain (42218 atoms), one
> additional water is molecule added in this complex. I don't know why this
> happen.
>
>
> Thanks in advance
>
> with regards
>
> R. A. Jeyaram
>
> Research Scholar
>
> Vellore Institute of Technology
>
> Tamil Nadu, India.
>
> ________________________________
> From: Elvis Martis <elvis_bcp.elvismartis.in>
> Sent: Wednesday, August 7, 2019 8:03:31 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] error during the calculation of MMPBSA
>
> Hi
> radiopt=0 should be placed in &pb and not in &general.
>
> On Tuesday, August 6, 2019, Jeyaram R A <ra.jeyaram.vit.ac.in> wrote:
>
> > Respected Sir,
> > I am adding the keyword radiopt =0 in my mmpbsa.in file. It shows
> > the input error as
> > "InputError: Unknown variable radiopt in &general". Can you please check
> > my input file. In the following I am attaching the mmpbsa.in file.
> > Thanks in advance
> > ________________________________
> > From: Jeyaram R A
> > Sent: Tuesday, August 6, 2019 10:20:38 PM
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] error during the calculation of MMPBSA
> >
> >
> > Respected Sir,
> >
> > I am adding the keyword radiopt =0 in my mmpbsa.in file. It shows
> > the input error as
> >
> > "InputError: Unknown variable radiopt in &general". Can you please check
> > my input file. In the following I am attaching the mmpbsa.in file.
> > Thanks in advance
> >
> >
> >
> >
> >
> > ________________________________
> > 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
> > > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> > --
> > Best Regards
> > Elvis Martis
> > Mumbai.
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> Best Regards
> Elvis Martis
> Mumbai.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Aug 06 2019 - 23:00:03 PDT
