No luck (see below), but what I don’t understand is that cpptraj as part of AmberTools never gave me any trouble to install/run. Why is the stand-alone version a problem?
./configure --buildlibs -macAccelerate -fftw3 gnu
...
Checking LAPACK/BLAS: Failed.
Error: LAPACK/BLAS 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 -o testp testp.cpp -framework Accelerate -lgfortran -lpthread -L/usr/local/opt/lapack/lib
Error: Error message follows:
Error: ld: library not found for -lgfortran
clang-11: error: linker command failed with exit code 1 (use -v to see invocation)
Maybe I should try my linux computer.
Best,
Matthew
> On Mar 30, 2022, at 8:44 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> *Message sent from a system outside of UConn.*
>
>
> ::big sigh::
>
> OSX is frustrating to develop for. Things that work in one version
> tend to break in the next. I don't really have a mac myself so it's
> hard to test these things.
>
> That said, there's one more thing I can think of for you can try: use
> the macAccelerate libs for Blas/lapack:
>
> ./configure --buildlibs -macAccelerate -fftw3 gnu
>
> On Wed, Mar 30, 2022 at 8:22 PM Matthew Guberman-Pfeffer
> <matthew.guberman-pfeffer.uconn.edu> wrote:
>>
>> That variable is defined, and I see stuff related to blas/lapack in that directory, so I gave it a try. Now I get:
>>
>> (AmberTools20) cpptraj >> ./configure --buildlibs --with-blas=$AMBERHOME --with-lapack=$AMBERHOME -fftw3 gnu
>> blas specified: /opt/anaconda3/envs/AmberTools20
>> lapack specified: /opt/anaconda3/envs/AmberTools20
>> 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: OK
>> dyld: Library not loaded: .rpath/libopenblas.0.dylib
>> Referenced from: /Users/matthewguberman-pfeffer/PersonalDIR/Desktop/Programs/cpptraj/./testp
>> Reason: image not found
>> ./configure: line 479: 33841 Abort trap: 6 ./testp > prog.out
>>
>> Error: Run of test program failed, compiled with: 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 -o testp testp.cpp -L/opt/anaconda3/envs/AmberTools20/lib -llapack -L/opt/anaconda3/envs/AmberTools20/lib -lblas -lgfortran -L/usr/local/opt/lapack/lib
>>
>>
>> Best,
>> Matthew
>>
>>
>>> On Mar 30, 2022, at 8:14 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>>>
>>> *Message sent from a system outside of UConn.*
>>>
>>>
>>> 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&data=04%7C01%7C%7C9e0a54e58cf7452e670e08da12afb7d6%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637842843159510311%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=cjExxfb9qvGQVz66ZAVwdyDCaqLF4sUYmAm2l07%2FdG0%3D&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&data=04%7C01%7C%7C9e0a54e58cf7452e670e08da12afb7d6%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637842843159510311%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=qVLNHZSwLGTivEQh%2FPMRe19mGHPVmd8bZhN7Q0%2Fg49E%3D&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&data=04%7C01%7C%7C9e0a54e58cf7452e670e08da12afb7d6%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637842843159510311%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=nXOhhXL4dZK8Xg3vh2B9RPRjjgMZ5qa6tPEcF6ghp5E%3D&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&data=04%7C01%7C%7C9e0a54e58cf7452e670e08da12afb7d6%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637842843159510311%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=nXOhhXL4dZK8Xg3vh2B9RPRjjgMZ5qa6tPEcF6ghp5E%3D&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&data=04%7C01%7C%7C9e0a54e58cf7452e670e08da12afb7d6%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637842843159510311%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=B1wcMKoHtpau5gic02g12V0z5ppyEuQSs0ijLJRc3GA%3D&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&data=04%7C01%7C%7C9e0a54e58cf7452e670e08da12afb7d6%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637842843159666558%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=aVHMqIlf4J359blpwXYvrsbb6aaBM9GcNRYaTy6zae4%3D&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&data=04%7C01%7C%7C9e0a54e58cf7452e670e08da12afb7d6%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637842843159666558%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=URb7EMjhoDoHp5e3%2FhTTAGzFWVR1AWIX4ZrXAFZ3UV8%3D&reserved=0
>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> AMBER mailing list
>>>>>>>>>>> AMBER.ambermd.org
>>>>>>>>>>>
>>>>>>>>>> https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=04%7C01%7C%7C9e0a54e58cf7452e670e08da12afb7d6%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637842843159666558%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=URb7EMjhoDoHp5e3%2FhTTAGzFWVR1AWIX4ZrXAFZ3UV8%3D&reserved=0
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> AMBER mailing list
>>>>>>>>>> AMBER.ambermd.org
>>>>>>>>>> https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=04%7C01%7C%7C9e0a54e58cf7452e670e08da12afb7d6%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637842843159666558%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=URb7EMjhoDoHp5e3%2FhTTAGzFWVR1AWIX4ZrXAFZ3UV8%3D&reserved=0
>>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> AMBER mailing list
>>>>>>>>> AMBER.ambermd.org
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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&data=04%7C01%7C%7C9e0a54e58cf7452e670e08da12afb7d6%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637842843159666558%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=URb7EMjhoDoHp5e3%2FhTTAGzFWVR1AWIX4ZrXAFZ3UV8%3D&reserved=0
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> AMBER mailing list
>>>>>>> AMBER.ambermd.org
>>>>>>> https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=04%7C01%7C%7C9e0a54e58cf7452e670e08da12afb7d6%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637842843159666558%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=URb7EMjhoDoHp5e3%2FhTTAGzFWVR1AWIX4ZrXAFZ3UV8%3D&reserved=0
>>>>>>
>>>>>> _______________________________________________
>>>>>> AMBER mailing list
>>>>>> AMBER.ambermd.org
>>>>>> https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=04%7C01%7C%7C9e0a54e58cf7452e670e08da12afb7d6%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637842843159666558%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=URb7EMjhoDoHp5e3%2FhTTAGzFWVR1AWIX4ZrXAFZ3UV8%3D&reserved=0
>>>>>
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=04%7C01%7C%7C9e0a54e58cf7452e670e08da12afb7d6%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637842843159666558%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=URb7EMjhoDoHp5e3%2FhTTAGzFWVR1AWIX4ZrXAFZ3UV8%3D&reserved=0
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=04%7C01%7C%7C9e0a54e58cf7452e670e08da12afb7d6%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637842843159666558%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=URb7EMjhoDoHp5e3%2FhTTAGzFWVR1AWIX4ZrXAFZ3UV8%3D&reserved=0
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=04%7C01%7C%7C9e0a54e58cf7452e670e08da12afb7d6%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637842843159666558%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=URb7EMjhoDoHp5e3%2FhTTAGzFWVR1AWIX4ZrXAFZ3UV8%3D&reserved=0
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=04%7C01%7C%7C9e0a54e58cf7452e670e08da12afb7d6%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637842843159666558%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=URb7EMjhoDoHp5e3%2FhTTAGzFWVR1AWIX4ZrXAFZ3UV8%3D&reserved=0
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
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Received on Wed Mar 30 2022 - 18:00:03 PDT
