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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Received on Wed Mar 30 2022 - 14:00:02 PDT
