Re: [AMBER] CPPTRAJ, Counting Per Residue Pair H-Bonding

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Wed, 30 Mar 2022 20:14:34 -0400

OK - seems like OSX makes it a pain to build lapack. Try this
(assuming AMBERHOME is set and AMBERHOME/lib contains blas/lapack):

./configure --buildlibs --with-blas=$AMBERHOME
--with-lapack=$AMBERHOME -fftw3 gnu

On Wed, Mar 30, 2022 at 7:36 PM Matthew Guberman-Pfeffer
<matthew.guberman-pfeffer.uconn.edu> wrote:
>
> Yes, here’s the file attached.
>
>
> > On Mar 30, 2022, at 7:31 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> >
> > *Message sent from a system outside of UConn.*
> >
> >
> > Are there any errors in
> > /Users/matthewguberman-pfeffer/PersonalDIR/Desktop/Programs/cpptraj/lapack_compile.log
> > ?
> >
> > On Wed, Mar 30, 2022 at 7:12 PM Matthew Guberman-Pfeffer
> > <matthew.guberman-pfeffer.uconn.edu> wrote:
> >>
> >> I downloaded from that link now. If I try with clang, I get:
> >>
> >> fftw3 enabled.
> >> C++ compiler (CXX) set to x86_64-apple-darwin13.4.0-clang++
> >> C compiler (CC) set to x86_64-apple-darwin13.4.0-clang
> >> Fortran compiler (FC) set to /opt/anaconda3/envs/AmberTools20/bin/x86_64-apple-darwin13.4.0-gfortran
> >>
> >> Testing C++ compiler: OK
> >> Testing C compiler: OK
> >> Testing Fortran compiler: OK
> >> Testing basic C++11 support: OK
> >> Testing system headers for C++11 support: OK
> >> Testing clang C++/Fortran linking: dyld: Library not loaded: @rpath/libgfortran.5.dylib
> >> Referenced from: /Users/matthewguberman-pfeffer/PersonalDIR/Desktop/Programs/cpptraj/./testp
> >> Reason: image not found
> >> ./configure: line 479: 23112 Abort trap: 6 ./testp > prog.out
> >>
> >> Error: Run of test program failed, compiled with: x86_64-apple-darwin13.4.0-clang++ -o testp testc.o testf.o -L/opt/anaconda3/envs/AmberTools20/lib/gcc/x86_64-apple-darwin13.4.0/9.3.0/../../../ -lgfortran -L/usr/local/opt/lapack/lib
> >>
> >> If I try with GNU, I get:
> >> (AmberTools20) cpptraj >> ./configure -fftw3 --buildlibs gnu
> >> fftw3 enabled.
> >> C++ compiler (CXX) set to x86_64-apple-darwin13.4.0-clang++
> >> C compiler (CC) set to x86_64-apple-darwin13.4.0-clang
> >> Fortran compiler (FC) set to /opt/anaconda3/envs/AmberTools20/bin/x86_64-apple-darwin13.4.0-gfortran
> >>
> >> Testing C++ compiler: OK
> >> Testing C compiler: OK
> >> Testing Fortran compiler: OK
> >> Testing basic C++11 support: OK
> >> Testing system headers for C++11 support: OK
> >> Enabled libraries will be built if not present.
> >> Checking BZLIB: OK
> >> Checking ZLIB: OK
> >> Checking NetCDF: Checking for bundled NetCDF: Downloading netcdf...
> >> --2022-03-30 19:10:26-- https://nam10.safelinks.protection.outlook.com/?url=ftp%3A%2F%2Fftp.unidata.ucar.edu%2Fpub%2Fnetcdf%2Fnetcdf-4.6.1.tar.gz&amp;data=04%7C01%7C%7C63aaaa87d7594c9f936708da12a575e5%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637842799097816378%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&amp;sdata=a0e%2BpvIZro2TbWxoRbdKjJ5LCG2D7pVejYt0O9IRTVg%3D&amp;reserved=0
> >> => ‘netcdf-4.6.1.tar.gz’
> >> Resolving ftp.unidata.ucar.edu (ftp.unidata.ucar.edu)... 128.117.149.10
> >> Connecting to ftp.unidata.ucar.edu (ftp.unidata.ucar.edu)|128.117.149.10|:21... connected.
> >> Logging in as anonymous ... Logged in!
> >> ==> SYST ... done. ==> PWD ... done.
> >> ==> TYPE I ... done. ==> CWD (1) /pub/netcdf ... done.
> >> ==> SIZE netcdf-4.6.1.tar.gz ... 5693557
> >> ==> PASV ... done. ==> RETR netcdf-4.6.1.tar.gz ... done.
> >> Length: 5693557 (5.4M) (unauthoritative)
> >>
> >> netcdf-4.6.1.tar.gz 100%[=====================================================================================================================>] 5.43M 2.25MB/s in 2.4s
> >>
> >> 2022-03-30 19:10:29 (2.25 MB/s) - ‘netcdf-4.6.1.tar.gz’ saved [5693557]
> >>
> >> Unpacking netcdf...
> >> Configuring netcdf... Success.
> >> ./get_library.sh: line 183: nproc: command not found
> >> MAKE_COMMAND is not set; set to 'make -j6'
> >> Compiling netcdf (may be time-consuming)... Success.
> >> Checking built NetCDF: OK
> >> Checking LAPACK/BLAS: Checking for bundled LAPACK/BLAS: Downloading lapack...
> >> --2022-03-30 19:11:02-- https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FReference-LAPACK%2Flapack%2Farchive%2Fv3.9.0.tar.gz&amp;data=04%7C01%7C%7C63aaaa87d7594c9f936708da12a575e5%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637842799097816378%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&amp;sdata=ySVETNFOYA2y8C72XqY00B0GmVJRWGvQPmj25K%2B6G%2Bo%3D&amp;reserved=0
> >> Resolving github.com (github.com)... 140.82.113.4
> >> Connecting to github.com (github.com)|140.82.113.4|:443... connected.
> >> HTTP request sent, awaiting response... 302 Found
> >> Location: https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcodeload.github.com%2FReference-LAPACK%2Flapack%2Ftar.gz%2Frefs%2Ftags%2Fv3.9.0&amp;data=04%7C01%7C%7C63aaaa87d7594c9f936708da12a575e5%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637842799097816378%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&amp;sdata=MqmNr%2B47C%2Fzj1OD7H7ZVjGfTPYNn5zWdpr9v2v6jfiE%3D&amp;reserved=0 [following]
> >> --2022-03-30 19:11:02-- https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcodeload.github.com%2FReference-LAPACK%2Flapack%2Ftar.gz%2Frefs%2Ftags%2Fv3.9.0&amp;data=04%7C01%7C%7C63aaaa87d7594c9f936708da12a575e5%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637842799097816378%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&amp;sdata=MqmNr%2B47C%2Fzj1OD7H7ZVjGfTPYNn5zWdpr9v2v6jfiE%3D&amp;reserved=0
> >> Resolving codeload.github.com (codeload.github.com)... 140.82.114.9
> >> Connecting to codeload.github.com (codeload.github.com)|140.82.114.9|:443... connected.
> >> HTTP request sent, awaiting response... 200 OK
> >> Length: unspecified [application/x-gzip]
> >> Saving to: ‘v3.9.0.tar.gz’
> >>
> >> v3.9.0.tar.gz [ <=> ] 7.18M 5.04MB/s in 1.4s
> >>
> >> 2022-03-30 19:11:04 (5.04 MB/s) - ‘v3.9.0.tar.gz’ saved [7534567]
> >>
> >> Unpacking lapack...
> >> Configuring lapack... (using generated make.inc) Success.
> >> ./get_library.sh: line 183: nproc: command not found
> >> MAKE_COMMAND is not set; set to 'make -j6'
> >> Compiling lapack (may be time-consuming)... Build failed.
> >> Check /Users/matthewguberman-pfeffer/PersonalDIR/Desktop/Programs/cpptraj/lapack_compile.log for errors.
> >> Error: Building LAPACK/BLAS failed.
> >>
> >>
> >>
> >> Best,
> >> Matthew
> >>> On Mar 30, 2022, at 7:05 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> >>>
> >>> *Message sent from a system outside of UConn.*
> >>>
> >>>
> >>> Hi,
> >>>
> >>> On Wed, Mar 30, 2022 at 4:59 PM Matthew Guberman-Pfeffer
> >>> <matthew.guberman-pfeffer.uconn.edu> wrote:
> >>>> Error: Unrecognized Option '—buildlibs'. Use '-h' or '--help' for help.
> >>>
> >>> This indicates you're using an older version. Make sure you're using
> >>> the GitHub version (https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FAmber-MD%2Fcpptraj&amp;data=04%7C01%7C%7C63aaaa87d7594c9f936708da12a575e5%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637842799097816378%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&amp;sdata=Cd1zFv5HfoD3bXQbWLBd4cqCGUtDH%2BfQa%2BbYX%2BUS0uc%3D&amp;reserved=0); this is the
> >>> only version with the new hbond matrix functionality.
> >>>
> >>> Once you've got the GitHub version, try
> >>>
> >>> ./configure -fftw3 --buildlibs clang
> >>>
> >>> Since it seems like you have clang and not GNU compilers.
> >>>
> >>> -Dan
> >>>
> >>>>
> >>>> Then, I tried:
> >>>> (AmberTools20) cpptraj >> ./configure -fftw3 gnu
> >>>> fftw3 enabled.
> >>>> C++ compiler (CXX) set to x86_64-apple-darwin13.4.0-clang++
> >>>> C compiler (CC) set to x86_64-apple-darwin13.4.0-clang
> >>>> Fortran compiler (FC) set to /opt/anaconda3/envs/AmberTools20/bin/x86_64-apple-darwin13.4.0-gfortran
> >>>>
> >>>> Testing C++ compiler: OK
> >>>> Testing C compiler: OK
> >>>> Testing Fortran compiler: OK
> >>>> Testing basic C++11 support: OK
> >>>> Testing system headers for C++11 support: OK
> >>>> Checking BZLIB: OK
> >>>> Checking ZLIB: OK
> >>>> Checking NetCDF: Checking for bundled NetCDF: OK
> >>>> Checking LAPACK/BLAS: Checking for bundled LAPACK/BLAS: Should CPPTRAJ attempt to build its own lapack? {y|n}: y
> >>>> Configuring lapack... (using generated make.inc) Success.
> >>>> ./get_library.sh: line 183: nproc: command not found
> >>>> MAKE_COMMAND is not set; set to 'make -j6'
> >>>> Compiling lapack (may be time-consuming)... Build failed.
> >>>> Check /Users/matthewguberman-pfeffer/PersonalDIR/Desktop/Programs/cpptraj/lapack_compile.log for errors.
> >>>> Error: Building LAPACK/BLAS failed.
> >>>>
> >>>> Best,
> >>>> Matthew
> >>>>
> >>>>
> >>>>> On Mar 30, 2022, at 4:54 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> >>>>>
> >>>>> *Message sent from a system outside of UConn.*
> >>>>>
> >>>>>
> >>>>> Hi,
> >>>>>
> >>>>> Try configure -fftw3 —buildlibs gnu
> >>>>>
> >>>>> -Dan
> >>>>>
> >>>>> On Wed, Mar 30, 2022 at 4:40 PM Matthew Guberman-Pfeffer <
> >>>>> matthew.guberman-pfeffer.uconn.edu> wrote:
> >>>>>
> >>>>>> Hi Dan,
> >>>>>>
> >>>>>> Thanks! I tried to install cpptraj from GitHub on my Mac, but had the
> >>>>>> below errors:
> >>>>>>
> >>>>>> I tried ./configure gnu -amberlib and got the below error:
> >>>>>>
> >>>>>> C++ compiler (CXX) set to x86_64-apple-darwin13.4.0-clang++
> >>>>>> C compiler (CC) set to x86_64-apple-darwin13.4.0-clang
> >>>>>> Fortran compiler (FC) set to
> >>>>>> /opt/anaconda3/envs/AmberTools20/bin/x86_64-apple-darwin13.4.0-gfortran
> >>>>>>
> >>>>>> Testing C++ compiler: OK
> >>>>>> Testing C compiler: OK
> >>>>>> Testing Fortran compiler: OK
> >>>>>> Testing basic C++11 support: OK
> >>>>>> Testing system headers for C++11 support: OK
> >>>>>> Using blas from /opt/anaconda3/envs/AmberTools20
> >>>>>> Using lapack from /opt/anaconda3/envs/AmberTools20
> >>>>>> Using netcdf from /opt/anaconda3/envs/AmberTools20
> >>>>>> Warning: Cannot link 'lapack' statically.
> >>>>>> Warning: Cannot link 'blas' statically.
> >>>>>> Checking BZLIB: OK
> >>>>>> Checking ZLIB: OK
> >>>>>> Checking NetCDF: Failed.
> >>>>>> Error: NetCDF build/link failed:
> >>>>>> x86_64-apple-darwin13.4.0-clang++ -Wall -O3 -march=core2
> >>>>>> -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE
> >>>>>> -fstack-protector-strong -O2 -pipe -stdlib=libc++
> >>>>>> -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 -isystem
> >>>>>> /opt/anaconda3/envs/AmberTools20/include -std=gnu++11 -
> >>>>>> I/opt/anaconda3/envs/AmberTools20/include -o testp testp.cpp
> >>>>>> /opt/anaconda3/envs/AmberTools20/lib/libnetcdf.a
> >>>>>> -L/usr/local/opt/lapack/lib
> >>>>>> Error: Error message follows:
> >>>>>> Error: Undefined symbols for architecture x86_64:
> >>>>>>
> >>>>>> I tried ./configure gnu and got the below error:
> >>>>>>
> >>>>>> C++ compiler (CXX) set to x86_64-apple-darwin13.4.0-clang++
> >>>>>> C compiler (CC) set to x86_64-apple-darwin13.4.0-clang
> >>>>>> Fortran compiler (FC) set to
> >>>>>> /opt/anaconda3/envs/AmberTools20/bin/x86_64-apple-darwin13.4.0-gfortran
> >>>>>>
> >>>>>> Testing C++ compiler: OK
> >>>>>> Testing C compiler: OK
> >>>>>> Testing Fortran compiler: OK
> >>>>>> Testing basic C++11 support: OK
> >>>>>> Testing system headers for C++11 support: OK
> >>>>>> Checking BZLIB: OK
> >>>>>> Checking ZLIB: OK
> >>>>>> Checking NetCDF: Checking for bundled NetCDF: OK
> >>>>>> Checking LAPACK/BLAS: Checking for bundled LAPACK/BLAS: Should
> >>>>>> CPPTRAJ attempt to build its own lapack? {y|n}: y
> >>>>>> Configuring lapack... (using generated make.inc) Success.
> >>>>>> ./get_library.sh: line 183: nproc: command not found
> >>>>>> MAKE_COMMAND is not set; set to 'make -j6'
> >>>>>> Compiling lapack (may be time-consuming)... Build failed.
> >>>>>> Check
> >>>>>> /Users/matthewguberman-pfeffer/PersonalDIR/Desktop/Programs/cpptraj/lapack_compile.log
> >>>>>> for errors.
> >>>>>> Error: Building LAPACK/BLAS failed.
> >>>>>>
> >>>>>> Best,
> >>>>>> Matthew
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>> On Mar 30, 2022, at 3:27 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> >>>>>>>
> >>>>>>> *Message sent from a system outside of UConn.*
> >>>>>>>
> >>>>>>>
> >>>>>>> Hi,
> >>>>>>>
> >>>>>>> I recently added this feature to GitHub cpptraj (version 6.4.5). Let
> >>>>>>> me know if it works for you if you get a chance to try it. More
> >>>>>>> details here:
> >>>>>> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FAmber-MD%2Fcpptraj%2Fpull%2F960&amp;data=04%7C01%7C%7C63aaaa87d7594c9f936708da12a575e5%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637842799097816378%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&amp;sdata=kYT%2FTUwxNqyZBHC1rs2xYHAdaamwzreqyKtcj3E7OMI%3D&amp;reserved=0
> >>>>>>>
> >>>>>>> -Dan
> >>>>>>>
> >>>>>>> On Wed, Mar 16, 2022 at 9:45 AM Matthew Guberman-Pfeffer
> >>>>>>> <matthew.guberman-pfeffer.uconn.edu> wrote:
> >>>>>>>>
> >>>>>>>> Dear Amber Community,
> >>>>>>>>
> >>>>>>>> I need to quantify the total number of H-bonds for each pair of
> >>>>>> residues in my protein. That would mean a 1321 x 1321 matrix. I am having
> >>>>>> trouble in writing a bash script to process the CPPTRAJ hbond output (e.g.
> >>>>>> All.UU.avg.dat) to compute each matrix element. I’ve thought of running
> >>>>>> CPPTRAJ for every possible pair of donormask and acceptormask, but this is
> >>>>>> truly an ugly brute-force approach. Does anyone have suggestions on how I
> >>>>>> can compute the total number of H-bonds between each pair of residues?
> >>>>>>>>
> >>>>>>>> Best,
> >>>>>>>> Matthew
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> _______________________________________________
> >>>>>>>> AMBER mailing list
> >>>>>>>> AMBER.ambermd.org
> >>>>>>>>
> >>>>>> https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&amp;data=04%7C01%7C%7C63aaaa87d7594c9f936708da12a575e5%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637842799097816378%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&amp;sdata=IN3JmdjAnv%2Bup%2BAYryZCw1lvXpBMZK21nX3eYNNnbDk%3D&amp;reserved=0
> >>>>>>>
> >>>>>>> _______________________________________________
> >>>>>>> AMBER mailing list
> >>>>>>> AMBER.ambermd.org
> >>>>>>>
> >>>>>> https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&amp;data=04%7C01%7C%7C63aaaa87d7594c9f936708da12a575e5%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637842799097816378%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&amp;sdata=IN3JmdjAnv%2Bup%2BAYryZCw1lvXpBMZK21nX3eYNNnbDk%3D&amp;reserved=0
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> AMBER mailing list
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> >>>>>>
> >>>>> _______________________________________________
> >>>>> AMBER mailing list
> >>>>> AMBER.ambermd.org
> >>>>> https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&amp;data=04%7C01%7C%7C63aaaa87d7594c9f936708da12a575e5%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637842799097816378%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&amp;sdata=IN3JmdjAnv%2Bup%2BAYryZCw1lvXpBMZK21nX3eYNNnbDk%3D&amp;reserved=0
> >>>>
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> >>>
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> >>
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> >
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Received on Wed Mar 30 2022 - 17:30:02 PDT
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