One more thing I missed,
After you have successfully located the file and edited it accordingly,
please don't forget to recompile AMBER.
Best Regards
Elvis
On Mon, 14 Dec 2020 at 17:05, Elvis Martis <elvis_bcp.elvismartis.in> wrote:
> 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
>> > > > > AMBER.ambermd.org
>> > > > > http://lists.ambermd.org/mailman/listinfo/amber
>> > > > >
>> > > > _______________________________________________
>> > > > 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
>> > > AMBER.ambermd.org
>> > > http://lists.ambermd.org/mailman/listinfo/amber
>> > >
>> > _______________________________________________
>> > 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
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
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Received on Mon Dec 14 2020 - 04:30:02 PST
