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://github.com/Amber-MD/cpptraj); 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%7Cf05b57dcb0944573cdf308da128f91e4%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637842705076813792%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=6SnXN2i3rSyfGNbmkyJl%2Bk1tNUG0jl6MUfBkMV%2FkxzQ%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%7Cf05b57dcb0944573cdf308da128f91e4%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637842705076813792%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=rvgruVV2XL5uOTd7GnCQCc%2FdX3WUf1pDL%2BQ30ZYX1zw%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%7Cf05b57dcb0944573cdf308da128f91e4%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637842705076813792%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=rvgruVV2XL5uOTd7GnCQCc%2FdX3WUf1pDL%2BQ30ZYX1zw%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%7Cf05b57dcb0944573cdf308da128f91e4%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637842705076813792%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=rvgruVV2XL5uOTd7GnCQCc%2FdX3WUf1pDL%2BQ30ZYX1zw%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%7Cf05b57dcb0944573cdf308da128f91e4%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637842705076813792%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=rvgruVV2XL5uOTd7GnCQCc%2FdX3WUf1pDL%2BQ30ZYX1zw%3D&reserved=0
>
> _______________________________________________
> 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
Received on Wed Mar 30 2022 - 16:30:02 PDT
