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
Received on Thu Nov 28 2019 - 05:00:02 PST
