Hi
Here is a solution in a different thread, you will have to edit the
mdread.f file. Please have a look at link below to know how to edit the
file and where to find it.
Re: [AMBER] bad atom type: Br from Jason Swails on 2011-11-11 (Amber
Archive Nov 2011) (ambermd.org)
<
http://archive.ambermd.org/201111/0370.html>
Best Regards
Elvis
On Mon, 14 Dec 2020 at 15:34, Vaibhav Dixit <vaibhavadixit.gmail.com> wrote:
> Dear All,
> I'm getting the following error message while trying to run MMPBSA.py in
> Amber20.
> It says that the receptor mask overwritten with default, which I don't know
> why it is doing even after I gave a specific receptor mask (1st residue is
> my ligand in the trajectory). It also gives the bad atom type error, that
> I got with Amber18 last month.
>
> >From the output files (attached), it is not clear what is the exact nature
> of the error, thus I have no clue how to proceed to fix the same.
> Can you please help me understand why the dry prmtop is not compatible?
> And how can I possibly attempt to get this analysis done?
> My mmpbsa input file is given below.
> Thanking you all in advance.
> Best regards
>
> mmpbsa input file:
> (base) [exx.c107739 mmpbsa-6701-tyr]$ more mmpbsa-decomp.in
> &general
> startframe=1, endframe=100, interval=5,
> verbose=2, keep_files=2, netcdf=1, receptor_mask=2-386,
> strip_mask=:387-16750,
> /
> &gb
> igb=5, saltcon=0.150,
> /
> &pb
> istrng=0.15, fillratio=4.0,
> /
> &decomp
> idecomp=1, print_res="56-57; 74-75; 167; 222; 225-227; 229-231; 272-273;
> 275-277; 336; 368; 370; 372-373"
> dec_verbose=1,
> /
>
>
> Error message on the terminal
> (base) [exx.c107739 mmpbsa-6701-tyr]$ MMPBSA.py -O -i mmpbsa-decomp.in -o
> mmpbs-rouf-6701-tyr.dat -do decomp-rouf-6701-tyr.dat -sp
> ../rouf-6701-tyr-solv.prmtop -cp ../rouf-6701-tyr-dry.prmtop -lp
> ../tyr-dry.prmtop -y ../rouf-6701-tyr-solv-prod300.nc -rp
> ../rouf-6701-nolig-dry.prmtop
> Loading and checking parameter files for compatibility...
>
> */home/exx/Downloads/amber20/lib/python3.8/site-packages/MMPBSA_mods/main.py:603:
> UserWarning: receptor_mask overwritten with default*
>
> warnings.warn('receptor_mask overwritten with default\n')
> cpptraj found! Using /home/exx/Downloads/amber20/bin/cpptraj
> sander found! Using /home/exx/Downloads/amber20/bin/sander
> Preparing trajectories for simulation...
> 20 frames were processed by cpptraj for use in calculation.
>
> Running calculations on normal system...
>
> Beginning GB calculations with /home/exx/Downloads/amber20/bin/sander
> calculating complex contribution...
> * bad atom type: M1*
> File "/home/exx/Downloads/amber20/bin/MMPBSA.py", line 100, in <module>
> app.run_mmpbsa()
> File
>
> "/home/exx/Downloads/amber20/lib/python3.8/site-packages/MMPBSA_mods/main.py",
> line 218, in run_mmpbsa
> self.calc_list.run(rank, self.stdout)
> File
>
> "/home/exx/Downloads/amber20/lib/python3.8/site-packages/MMPBSA_mods/calculation.py",
> line 82, in run
> calc.run(rank, stdout=stdout, stderr=stderr)
> File
>
> "/home/exx/Downloads/amber20/lib/python3.8/site-packages/MMPBSA_mods/calculation.py",
> line 156, in run
> raise CalcError('%s failed with prmtop %s!' % (self.program,
> CalcError: /home/exx/Downloads/amber20/bin/sander failed with prmtop
> ../rouf-6701-tyr-dry.prmtop!
> Exiting. All files have been retained.
>
> --
>
> Regards,
>
> Dr. Vaibhav A. Dixit,
>
> Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
> University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
> AND
> Assistant Professor,
> Department of Pharmacy,
> ▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
> Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
> VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
> India.
> Phone No. +91 1596 255652, Mob. No. +91-7709129400,
> Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
> http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
> https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
>
> ORCID ID: https://orcid.org/0000-0003-4015-2941
>
> http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
>
> P Please consider the environment before printing this e-mail
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Received on Mon Dec 14 2020 - 02:30:02 PST
