OK.
Have you compiled AMBER20 using the legacy configure method or the new
cmake method?
If you have using the new cmake method of compilation, then I guess you
should find that file in amber20_src/AmberTools/src/sander/mdread2.F90.
if you have compiled using the legacy method, then you files should in the
path where I sent previously.
Best Regards
Elvis
On Mon, 14 Dec 2020 at 16:55, Vaibhav Dixit <vaibhavadixit.gmail.com> wrote:
> Dear All and Elivs,
> I'm afraid, I still can't find this file inside the AmberTools folder,
> there is no folder by the same sander.
> All tests passed while installing Amber20, thus I think there is some
> confusion regarding the directory structure and file locations in Amber18
> and Amber20 as well.
> Please let me know if you know the fix to this as well.
> thank you and best regards.
>
> (base) [exx.c107739 amber20]$ ls
> $AMBERHOME/AmberTools/src/sander/mdread2.F90
> ls: cannot access
> /home/exx/Downloads/amber20/AmberTools/src/sander/mdread2.F90: No such file
> or directory
> (base) [exx.c107739 amber20]$ cd AmberTools/src/
> (base) [exx.c107739 src]$ ls -arlth
> total 28K
> drwxrwxr-x. 3 exx exx 4.0K Dec 4 15:17 cpptraj
> drwxrwxr-x. 3 exx exx 4.0K Dec 4 15:17 mm_pbsa
> drwxrwxr-x. 3 exx exx 4.0K Dec 4 15:17 FEW
> drwxrwxr-x. 3 exx exx 4.0K Dec 4 15:17 pytraj
> drwxrwxr-x. 7 exx exx 4.0K Dec 4 15:25 ..
> -rw-r--r--. 1 exx exx 1.9K Dec 4 17:26 config.h
> drwxrwxr-x. 6 exx exx 4.0K Dec 4 17:45 .
>
> On Mon, Dec 14, 2020 at 7:46 PM Elvis Martis <elvis_bcp.elvismartis.in>
> wrote:
>
> > Hi
> > Sorry my bad. For AMBER20
> > you can look in
> > $AMBERHOME/AmberTools/src/sander/mdread2.F90
> > Start looking from line number 1508 (this should be same unless there
> were
> > changes made earlier)
> > this line starts with " else if ( gbsa == 2 ) then"
> >
> > Best Regards
> > Elvis
> >
> >
> >
> > On Mon, 14 Dec 2020 at 15:57, Vaibhav Dixit <vaibhavadixit.gmail.com>
> > wrote:
> >
> > > Dear All,
> > > I got this suggestion earlier last month also.
> > > But to my surprise, I can't find these specified folders and files in
> the
> > > expected locations.
> > > I ran a find command to search for the mdread.f file, but it is not
> found
> > > anywhere inside amber20 folder and subfolders.
> > > This command works and finds other files as shown below.
> > >
> > > Please do let me know what I'm missing to understand here.
> > > thanks
> > >
> > > (base) [exx.c107739 amber20]$ ls -arlth
> > > total 128K
> > > -rw-r--r--. 1 exx exx 7.5K Dec 6 2018 GNU_LGPL_v3
> > > -rwxr-xr-x. 1 exx exx 116 Dec 6 2018 amber-interactive.sh
> > > -rw-r--r--. 1 exx exx 1.1K Apr 28 2020 Makefile
> > > -rw-r--r--. 1 exx exx 37K Apr 28 2020 LICENSE
> > > drwxrwxr-x. 8 exx exx 4.0K Dec 4 15:17 licenses
> > > drwxrwxr-x. 2 exx exx 4.0K Dec 4 15:17 doc
> > > drwxrwxr-x. 19 exx exx 4.0K Dec 4 15:17 miniconda
> > > drwxrwxr-x. 3 exx exx 4.0K Dec 4 15:17 share
> > > drwxrwxr-x. 9 exx exx 4.0K Dec 4 15:17 benchmarks
> > > drwxrwxr-x. 16 exx exx 4.0K Dec 4 15:17 dat
> > > drwxrwxr-x. 7 exx exx 4.0K Dec 4 15:25 AmberTools
> > > -rw-r--r--. 1 exx exx 1.9K Dec 4 17:26 config.h
> > > drwxrwxr-x. 8 exx exx 4.0K Dec 10 15:54 logs
> > > drwxrwxr-x. 157 exx exx 4.0K Dec 10 15:58 test
> > > -rwxr-xr-x. 1 exx exx 1.8K Dec 10 20:38 amber.sh
> > > -rwxr-xr-x. 1 exx exx 1.9K Dec 10 20:38 amber.csh
> > > drwxrwxr-x. 15 exx exx 4.0K Dec 10 21:50 .
> > > drwxr-xr-x. 2 exx exx 4.0K Dec 10 21:50 include
> > > drwxrwxr-x. 4 exx exx 4.0K Dec 10 21:50 lib64
> > > drwxr-xr-x. 4 exx exx 4.0K Dec 10 21:50 lib
> > > drwxrwxr-x. 3 exx exx 4.0K Dec 10 21:50 bin
> > > drwxr-xr-x. 24 exx exx 4.0K Dec 12 12:13 ..
> > > (base) [exx.c107739 amber20]$ cd AmberTools/
> > > (base) [exx.c107739 AmberTools]$ ls -arlth
> > > total 28K
> > > drwxrwxr-x. 3 exx exx 4.0K Dec 4 15:17 benchmarks
> > > drwxrwxr-x. 6 exx exx 4.0K Dec 4 15:17 examples
> > > drwxrwxr-x. 3 exx exx 4.0K Dec 4 15:25 .pytest_cache
> > > drwxrwxr-x. 7 exx exx 4.0K Dec 4 15:25 .
> > > drwxrwxr-x. 6 exx exx 4.0K Dec 4 17:45 src
> > > drwxrwxr-x. 15 exx exx 4.0K Dec 10 21:50 ..
> > > drwxrwxr-x. 65 exx exx 4.0K Dec 10 21:59 test
> > > (base) [exx.c107739 AmberTools]$ cd ..
> > > (base) [exx.c107739 amber20]$ find . -name mdread.f
> > > (base) [exx.c107739 amber20]$ find . -name amber.sh
> > > ./amber.sh
> > > (base) [exx.c107739 amber20]$ find . -name am1bcc
> > > ./bin/am1bcc
> > > ./bin/wrapped_progs/am1bcc
> > >
> > > On Mon, Dec 14, 2020 at 7:14 PM Elvis Martis <elvis_bcp.elvismartis.in
> >
> > > wrote:
> > >
> > > > 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
> > > > > _______________________________________________
> > > > > AMBER mailing list
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> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
> > > > _______________________________________________
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> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > >
> > >
> > > --
> > >
> > > 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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> > > AMBER.ambermd.org
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> > >
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> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
>
> 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
> _______________________________________________
> AMBER mailing list
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>
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Received on Mon Dec 14 2020 - 04:30:02 PST
