Hello,
I haven't received any files yet.
Best Regards
On Thu, 28 Nov 2019 at 18:29, Nisha Amarnath Jonniya <
phd1601271002.iiti.ac.in> wrote:
> Dear Sir,
>
> Is there any solutions for the complex?
>
>
>
> Regards
>
> On Fri, 22 Nov 2019, 11:21 am Nisha Amarnath Jonniya, <
> phd1601271002.iiti.ac.in> wrote:
>
> > Dear Sir,
> >
> > Please find the attached files.
> > com-complex
> > rec-receptor
> > lignad
> >
> > On Fri, Nov 22, 2019 at 10:09 AM Elvis Martis <elvis_bcp.elvismartis.in>
> > wrote:
> >
> >> Hello
> >> Could you send the prmtop files and just one of two frames (as rst) off
> >> the
> >> list?
> >> Best Regards
> >>
> >>
> >>
> >> On Fri, 22 Nov 2019 at 10:00, Nisha Amarnath Jonniya <
> >> phd1601271002.iiti.ac.in> wrote:
> >>
> >> > Dear Sir,
> >> >
> >> > I tried changing the mdread2.F90 file with 'Mn"
> >> >
> >> > else if (atype == 'Mn') then x(l165-1+i) = 1.69d0 +
> 1.4d0*
> >> >
> >> > and recompiled and run.
> >> >
> >> > But the same error is coming.
> >> > * in decom.in I am including MN residue number in
> "print_res="1-276".
> >> >
> >> >
> >> >
> >> >
> >> > ############*ERROR*################
> >> > Loading and checking parameter files for compatibility...
> >> > sander found! Using /home/parimal4/Software/amber18/bin/sander
> >> > cpptraj found! Using /home/parimal4/Software/amber18/bin/cpptraj
> >> > Preparing trajectories for simulation...
> >> > 100 frames were processed by cpptraj for use in calculation.
> >> >
> >> > Running calculations on normal system...
> >> >
> >> > Beginning GB calculations with
> >> /home/parimal4/Software/amber18/bin/sander
> >> > calculating complex contribution...
> >> > bad atom type: Mn
> >> > bad atom type: Mn
> >> > bad atom type: Mn
> >> > File "/home/parimal4/Software/amber18/bin/MMPBSA.py.MPI", line 100,
> in
> >> > <module>
> >> > bad atom type: Mn
> >> > File "/home/parimal4/Software/amber18/bin/MMPBSA.py.MPI", line 100,
> in
> >> > <module>
> >> > bad atom type: Mn
> >> > File "/home/parimal4/Software/amber18/bin/MMPBSA.py.MPI", line 100,
> in
> >> > <module>
> >> > app.run_mmpbsa()
> >> > File
> >> >
> >> >
> >>
> "/home/parimal4/Software/amber18/lib/python2.7/site-packages/MMPBSA_mods/main.py",
> >> > line 218, in run_mmpbsa
> >> > app.run_mmpbsa()
> >> > File
> >> >
> >> >
> >>
> "/home/parimal4/Software/amber18/lib/python2.7/site-packages/MMPBSA_mods/main.py",
> >> > line 218, in run_mmpbsa
> >> > app.run_mmpbsa()
> >> > File
> >> >
> >> >
> >>
> "/home/parimal4/Software/amber18/lib/python2.7/site-packages/MMPBSA_mods/main.py",
> >> > line 218, in run_mmpbsa
> >> > bad atom type: Mn
> >> > bad atom type: Mn
> >> > self.calc_list.run(rank, self.stdout)
> >> > File
> >> >
> >> >
> >>
> "/home/parimal4/Software/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
> >> > line 82, in run
> >> >
> >> >
> >> >
> >> >
> >> > On Thu, Nov 21, 2019 at 7:37 PM David A Case <david.case.rutgers.edu>
> >> > wrote:
> >> >
> >> > > On Thu, Nov 21, 2019, Nisha Amarnath Jonniya wrote:
> >> > > >
> >> > > > I checked all my PDB files as well as pdf files from all
> trajectory,
> >> > and
> >> > > >"MN" is written everywhere and not "Mn".
> >> > >
> >> > > This is expected. Atom types are not recorded in PDB files.
> >> > >
> >> > > >But in complex.prmtop Mn2+ is showing.
> >> > >
> >> > > This is also expected.
> >> > >
> >> > > >and If I run decompose without MN it is running, giving no error.
> >> > >
> >> > > >> > I have added the lines as mentioned in mdread2.F90 file
> >> > > >> >
> >> > > >> > ########################3
> >> > > >> > else if (atype == 'F') then
> >> > > >> > x(l165-1+i) = 1.47d0 + 1.4d0
> >> > > >> > x(l170-1+i) = 0.68563d0
> >> > > >> > x(l175-1+i) = -0.1868d0
> >> > > >> > x(l180-1+i) = -0.00135573d0
> >> > > >> > x(l185-1+i) = 0.00023743d0
> >> > > >> >
> >> > > >> > *else if (atype == 'MN') then x(l165-1+i) =
> 1.69d0
> >> +
> >> > > 1.4d0*
> >> > > ^^^^^
> >> > >
> >> > > If you have not done so, change "MN" here to "Mn", recompile, and
> see
> >> if
> >> > > anything changes.
> >> > >
> >> > > ...dac
> >> > >
> >> > >
> >> > > _______________________________________________
> >> > > AMBER mailing list
> >> > > AMBER.ambermd.org
> >> > > http://lists.ambermd.org/mailman/listinfo/amber
> >> > >
> >> >
> >> >
> >> > --
> >> >
> >> > Nisha Amarnath Jonniya
> >> > PhD Research Scholar
> >> > Biosciences and Biomedical Engineering
> >> > Indian Institute of Technology, Indore
> >> > 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
> >>
> >
> >
> > --
> >
> > Nisha Amarnath Jonniya
> > PhD Research Scholar
> > Biosciences and Biomedical Engineering
> > Indian Institute of Technology, Indore
> > 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
Received on Thu Nov 28 2019 - 05:30:02 PST
