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 19:12:06 -0400

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-- ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.6.1.tar.gz
           => ‘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://github.com/Reference-LAPACK/lapack/archive/v3.9.0.tar.gz
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://codeload.github.com/Reference-LAPACK/lapack/tar.gz/refs/tags/v3.9.0 [following]
--2022-03-30 19:11:02-- https://codeload.github.com/Reference-LAPACK/lapack/tar.gz/refs/tags/v3.9.0
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%7Cbb0dd77f17d447c200ad08da12a1dbf7%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637842783647669025%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=AZPqAHW7xNt2OpAdSesgIX3lvTnkdkNFTTamlM5YVpY%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%7Cbb0dd77f17d447c200ad08da12a1dbf7%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637842783647669025%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=QhUPrwlelvtKlQBOH0TDpnqBQr0b7MZhjMrND0Ntjck%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
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
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>>>>>
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>>>>
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Received on Wed Mar 30 2022 - 16:30:02 PDT