chap

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Issue using the simg file

4

Hi, I am trying to use CHAP with singularity image. But it give the following error. I am using singularity image with Mac, uisng SingularityCE vagrant box with ubuntu 18.04,...

vinnu0143

Hello, I have been recently calculating the pore profile of a membrane protein, and I encountered an error: **chap -f closed.pdb -s closed.pdb -hydrophob-database user -hydrophob-json colour_scal.json** Standard library runtime...

aashuph16221

Issue with "Make" command

11

Hi sir, I am trying to install chap 0.9.1 on my workstation which is the Ubuntu 18.04.5 LTS and the gromacs version is 2020.5. Following the installation guide, I first...

joe781114

Errors related to make command, boost libraries and std cpp libraries while compiling CHAP

2

I'm trying to install CHAP version_0_9_1 and during the make command, I get this error: ``` (python3.11) bburendei@solaire:~/apps/CHAP/chap-version_0_9_1/build$ make [ 6%] Built target googletest Consolidate compiler generated dependencies of target...

batuujin

cmake error

3

In file included from /home/vrdl/Downloads/chap-master/src/aggregation/boltzmann_energy_calculator.cpp:25: /home/vrdl/Downloads/chap-master/include/aggregation/boltzmann_energy_calculator.hpp:30:10: fatal error: gromacs/utility/real.h: No such file or directory 30 | #include "gromacs/utility/real.h" | ^~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. make[2]: *** [CMakeFiles/chap.dir/build.make:63: CMakeFiles/chap.dir/src/aggregation/boltzmann_energy_calculator.cpp.o] Error 1 make[1]: ***...

DehuryB

Bumps [addressable](https://github.com/sporkmonger/addressable) from 2.5.1 to 2.8.1. Changelog Sourced from addressable's changelog. Addressable 2.8.1 refactor Addressable::URI.normalize_path to address linter offenses (#430) remove redundant colon in Addressable::URI::CharacterClasses::AUTHORITY regex (#438) update gemspec to...

dependabot[bot]

Plot against z-coordinates

1

Hi CHAP team, I have 2 CHAP profiles for two aligned ion channels. The channels are different in height and therefore have different centres of mass but their channels are...

askusay

Issues with python plotting graphs

4

Hello, After running chap and selecting water to analyze, I created the free energy profile, hydrophobicity profile, radius profile and solvent number density profile graphs from here: https://www.channotation.org/docs/plotting_python/ The free...

cgseitz

Standard library logic error (bug): (exception type: St12out_of_range) vector::_M_range_check: __n (which is 2) >= this->size() (which is 2)

12

Hello, I have tried running CHAP with this command: ``` chap -f ../../solvated_pores.trr -s ../../solvated_pores.pdb -sel-pathway 1 -sel-solvent 'Water' -pf-cutoff 0 -pf-init-probe-pos 133 112 70 ``` If I set the...

cgseitz

"Number of frames read does not equal numberof frames analyised."

1

Hello, Great tool you have built, thank you very much. I have compiled in a VM, and had it working on some small scale data, but have recently been getting...

jonah-lc