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%7C722a6744098740f71aaa08da12836e74%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637842652940616131%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=rS0A3wHi%2Fxd%2FvEJeXhDC6krW2sKG7Pao%2Bw%2B7Wjdvqto%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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> >> AMBER.ambermd.org
> >>
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> >
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Received on Wed Mar 30 2022 - 14:00:02 PDT
