Dear All and Elivs,
OK, now I got the file in amber20_src/AmberTools/src/sander.
I have made the following changes (in bold), and then set DMPI and DCUDA
both =FALSE and then ran run_make script.
But I get the error shown at the end.
Can you please check and help me understand what corrections to me to these
lines?
Thanks a lot and best regards.
x(L165-1+i) = 1.10d0 + 1.4d0
else if (atomicnumber .eq. 12) then
! Mg radius = 0.99A: ref. 21 in J. Chem. Phys. 1997, 107,
5422
! Mg radius = 1.18A: ref. 30 in J. Chem. Phys. 1997, 107,
5422
! Mg radius = 1.45A: Aqvist 1992
x(L165-1+i) = 1.18d0 + 1.4d0
*# else# write( 0,* ) 'bad atom type: ',atype#
FATAL_ERROR*
* else if (atomicnumber .eq. 23) then ! Fe radius
= 1.386A: ref. IOD set for Fe3+ ion in TIP3P water from Li et al. JPCB,
2015, 119, 883 x(L165-1+i) = 1.386d0 + 1.4d0*
end if
*Error with run_cmake script*
(base) [exx.c107739 build]$ gedit run_cmake &
[2] 16544
(base) [exx.c107739 build]$ make install
[ 0%] Built target ucpp
[ 0%] Built target fftw3_threads_obj
[ 1%] Built target fftw_api
[ 1%] Built target dft
[ 1%] Built target dft_scalar
[ 2%] Built target dft_scalar_codelets
[ 5%] Built target dft_sse2_codelets
[ 5%] Built target rdft
[ 5%] Built target rdft_scalar
[ 7%] Built target rdft_scalar_r2cb
[ 8%] Built target rdft_scalar_r2cf
[ 8%] Built target rdft_scalar_r2r
[ 8%] Built target rdft_sse2_codelets
[ 9%] Built target fftw_kernel
[ 9%] Built target reodft
[ 9%] Built target simd_support
[ 9%] Built target fftw
[ 9%] Built target libfftw_bench
[ 9%] Built target fftw_benchmark_common_obj
[ 9%] Built target fftw_benchmark
[ 9%] Built target fftw_wisdom
[ 9%] Built target fftw_mpi
[ 9%] Built target fftw_mpi_benchmark
[ 9%] Built target dispatch
[ 9%] Built target netcdf3
[ 9%] Built target netcdf
[ 10%] Built target ncgen
[ 10%] Built target ncgen3
[ 10%] Built target nccopy
[ 10%] Built target ncdump
[ 11%] Built target netcdff
[ 11%] Built target xblas_build
[ 12%] Built target blas
[ 15%] Built target lapack
[ 16%] Built target arpack
[ 19%] Built target pnetcdf_fortran_obj
[ 19%] Built target pnetcdf_c_obj
[ 19%] Built target pnetcdf
[ 19%] Built target ncvalid
[ 19%] Built target boost_build
[ 19%] Built target amber_common
[ 20%] Built target rism
[ 20%] Built target libpbsa
[ 20%] Built target sff_rism_interface
[ 20%] Built target sff_lex
[ 20%] Built target dsarpack_obj
[ 20%] Built target sff
[ 21%] Built target gbnsr6
[ 21%] Built target cifparse
[ 22%] Built target addles
[ 23%] Built target rism_mpi
[ 23%] Built target sander_rism_interface
[ 25%] Built target sqm_common
[ 25%] Built target libsqm
[ 26%] Built target sff_fortran
[ 26%] Building Fortran object
AmberTools/src/sander/CMakeFiles/sander_base_obj.dir/mdread.F90.o
/home/exx/Downloads/amber20_src/AmberTools/src/sander/mdread2.F90:1571.1:
Included at
/home/exx/Downloads/amber20_src/AmberTools/src/sander/mdread.F90:24:
\xC2\xA0 \xC2\xA0 \xC2\xA0 \xC2\xA0 \xC2\xA0 \xC2\xA0 \xC2\xA0! \xC2\xA0Fe
rad
1
Error: Invalid character in name at (1)
/home/exx/Downloads/amber20_src/AmberTools/src/sander/mdread2.F90:1572.1:
Included at
/home/exx/Downloads/amber20_src/AmberTools/src/sander/mdread.F90:24:
\xC2\xA0 \xC2\xA0 \xC2\xA0 \xC2\xA0 \xC2\xA0 \xC2\xA0 \xC2\xA0 x(L165-1+i)
= 1
1
Error: Invalid character in name at (1)
make[2]: ***
[AmberTools/src/sander/CMakeFiles/sander_base_obj.dir/mdread.F90.o] Error 1
make[1]: *** [AmberTools/src/sander/CMakeFiles/sander_base_obj.dir/all]
Error 2
make: *** [all] Error 2
[2]+ Done gedit run_cmake
On Mon, Dec 14, 2020 at 8:36 PM Elvis Martis <elvis_bcp.elvismartis.in>
wrote:
> 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
> >>
> >
> _______________________________________________
> 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/
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http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
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Received on Mon Dec 14 2020 - 05:00:02 PST
