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
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> > >
> >
> >
> > --
> >
> > 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
> >
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>
--
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 - 03:30:01 PST
