Re: [AMBER] CPPTRAJ, Counting Per Residue Pair H-Bonding from Matthew Guberman-Pfeffer on 2022-03-30 (Amber Archive Mar 2022)

From: Matthew Guberman-Pfeffer <matthew.guberman-pfeffer.uconn.edu>
Date: Wed, 30 Mar 2022 19:34:19 -0400

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%7C63aaaa87d7594c9f936708da12a575e5%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637842799097816378%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=a0e%2BpvIZro2TbWxoRbdKjJ5LCG2D7pVejYt0O9IRTVg%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%7C63aaaa87d7594c9f936708da12a575e5%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637842799097816378%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=ySVETNFOYA2y8C72XqY00B0GmVJRWGvQPmj25K%2B6G%2Bo%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%7C63aaaa87d7594c9f936708da12a575e5%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637842799097816378%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=MqmNr%2B47C%2Fzj1OD7H7ZVjGfTPYNn5zWdpr9v2v6jfiE%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%7C63aaaa87d7594c9f936708da12a575e5%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637842799097816378%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=MqmNr%2B47C%2Fzj1OD7H7ZVjGfTPYNn5zWdpr9v2v6jfiE%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%7C63aaaa87d7594c9f936708da12a575e5%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637842799097816378%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=Cd1zFv5HfoD3bXQbWLBd4cqCGUtDH%2BfQa%2BbYX%2BUS0uc%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%7C63aaaa87d7594c9f936708da12a575e5%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637842799097816378%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=kYT%2FTUwxNqyZBHC1rs2xYHAdaamwzreqyKtcj3E7OMI%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
>>>>>>>>
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>>>>>>>
>>>>>>> _______________________________________________
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>>>>>>>
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>>>>>>
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>>>>>>
>>>>> _______________________________________________
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>>>>
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>>>
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>>
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application/octet-stream attachment: lapack_compile.log

Received on Wed Mar 30 2022 - 17:00:03 PDT