Unable to install in LinuxMint

[debanjansen48]

I follow all the instructions given in installation webpage. http://sstmap.org/2019/12/06/getting-started/.

it return following Error.

running build_ext
building '_sstmap_ext' extension
creating build/temp.linux-x86_64-cpython-310
creating build/temp.linux-x86_64-cpython-310/sstmap
gcc -pthread -B /home/debanjan/miniconda3/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/debanjan/miniconda3/include -fPIC -O2 -isystem /home/debanjan/miniconda3/include -fPIC -I/home/debanjan/.local/lib/python3.10/site-packages/numpy/core/include -I/home/debanjan/miniconda3/include/python3.10 -c sstmap/_sstmap_ext.c -o build/temp.linux-x86_64-cpython-310/sstmap/_sstmap_ext.o
sstmap/_sstmap_ext.c:40:10: fatal error: gsl/gsl_linalg.h: No such file or directory
40 | #include <gsl/gsl_linalg.h>
| ^~~~~~~~~~~~~~~~~~
compilation terminated.
error: command '/usr/bin/gcc' failed with exit code 1

As mentioned to use GCC 7. I tried to install GCC G+=7 fut failed its not available.
**conda install -c conda-forge gcc=7
Collecting package metadata (current_repodata.json): done
Solving environment: unsuccessful initial attempt using frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): done
Solving environment: unsuccessful initial attempt using frozen solve. Retrying with flexible solve.

PackagesNotFoundError: The following packages are not available from current channels:

• gcc=7

Current channels:

• https://conda.anaconda.org/conda-forge/linux-64
• https://conda.anaconda.org/conda-forge/noarch
• https://repo.anaconda.com/pkgs/main/linux-64
• https://repo.anaconda.com/pkgs/main/noarch
• https://repo.anaconda.com/pkgs/r/linux-64
• https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

https://anaconda.org

and use the search bar at the top of the page.**

tried to install using sudo apt install gcc g++7
but package not found.

i tried conda install -c solvationtools sstmap

but its failed to install sstmap.
**sstmap) debanjan@debanjan:~/Downloads/SSTMap$ conda install -c solvationtools sstmap
Collecting package metadata (current_repodata.json): done
Solving environment: unsuccessful initial attempt using frozen solve. Retrying with flexible solve.
Solving environment: unsuccessful attempt using repodata from current_repodata.json, retrying with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: unsuccessful initial attempt using frozen solve. Retrying with flexible solve.
Solving environment: /
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.
failed

UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:

Specifications:

• sstmap -> python[version='>=3.10,<3.11.0a0|>=3.11,<3.12.0a0|>=3.8,<3.9.0a0|>=3.9,<3.10.0a0|>=3.7,<3.8.0a0']

Your python: python=3.6

If python is on the left-most side of the chain, that's the version you've asked for.
When python appears to the right, that indicates that the thing on the left is somehow
not available for the python version you are constrained to. Note that conda will not
change your python version to a different minor version unless you explicitly specify
that.

The following specifications were found to be incompatible with your system:

• feature:/linux-64::__glibc==2.35=0
• feature:|@/linux-64::__glibc==2.35=0
• sstmap -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']

Your installed version is: 2.35**

Please assist me how to resolve the issue.

[VjayMolino]

To answer your inquiry, you would need to install libgsl and a gcc compiler to proceed with the installation. For gsl, you can use the command 'sudo apt install libgsl-dev,' and for installing gcc on Linux Mint, you can follow this article: https://idroot.us/install-gcc-linux-mint-20/.

[debanjansen48]

yes also installed kiwisolver>=1.0.1. And it installed. Thanks. The issue solved. Thanks a lot

[debanjansen48]

but during test encountered by following error

(sstmap) debanjan@debanjan:~/Downloads/sstmap_test_suite$ make test_quick
cd tests/; python quick_test.py
Testing: amber
Initializing ...
Obtaining non-bonded parameters for the system ...
Total time running generate_nonbonded_params: 0.09 seconds
Done.
Assigning hydrogen bond types ...
Total time running assign_hb_types: 0.03 seconds
Done.
Initializing ...
Total time running init: 0.68 seconds
System information:
Parameter file: /home/debanjan/Downloads/sstmap_test_suite/platforms/amber/testcase.prmtop

Trajectory: /home/debanjan/Downloads/sstmap_test_suite/platforms/amber/md100ps.nc

Frames: 100, Total Atoms: 3026, Waters: 1001, Solute Atoms: 23

Grid information:
GIST grid center: 18.030 17.173 17.058

GIST grid dimensions: 48 48 48

GIST grid spacing: 0.500 A^3

Total referenced orientational entropy of the grid: dTSorient = -226.37442 kcal/mol, Nf=100
Total referenced translational entropy of the grid: dTStrans = -101.78446 kcal/mol, Nf=100
Total 6d if all one vox: -1.90546 kcal/mol
Total t if all one vox: -0.26787 kcal/mol
Total o if all one vox: -0.34450 kcal/mol
Total time running calculate_entropy: 0.09 seconds
Total time running calculate_grid_quantities: 30.63 seconds
Writing voxel data ...
Total time running write_data: 2.18 seconds
Summary of main calculations:
Number of frames processed: 100
Average number of water molecules over the grid: 199
Total Solute-Water Energy over the grid: -120.568504
Total Water-Water Energy over the grid: -1892.259424
Generating dx files ...
Total time running generate_dx_files: 1.30 seconds
Checking grid and voxel placement ...
Passed
Checking: n_wat
Passed
/home/debanjan/Downloads/sstmap_test_suite/platforms/amber/gist_output/testcase_dTSorient-dens.dx /home/debanjan/Downloads/sstmap_test_suite/ref_calcs/gist-dTSorient-dens.dx

Arrays are not almost equal to 3 decimals

Mismatch: 4.65%
Max absolute difference: 1.058384
Max relative difference: 1552.44073161
x: array([0., 0., 0., ..., 0., 0., 0.])
y: array([0., 0., 0., ..., 0., 0., 0.])
/home/debanjan/Downloads/sstmap_test_suite/platforms/amber/gist_output/testcase_Esw-dens.dx /home/debanjan/Downloads/sstmap_test_suite/ref_calcs/gist-Esw-dens.dx
Passed!
/home/debanjan/Downloads/sstmap_test_suite/platforms/amber/gist_output/testcase_dTSsix-dens.dx /home/debanjan/Downloads/sstmap_test_suite/ref_calcs/gist-dTSsix-dens.dx

Arrays are not almost equal to 3 decimals

Mismatch: 14.1%
Max absolute difference: 1.2515201
Max relative difference: 2804.28400168
x: array([0., 0., 0., ..., 0., 0., 0.])
y: array([0., 0., 0., ..., 0., 0., 0.])
/home/debanjan/Downloads/sstmap_test_suite/platforms/amber/gist_output/testcase_gO.dx /home/debanjan/Downloads/sstmap_test_suite/ref_calcs/gist-gO.dx
Passed!
/home/debanjan/Downloads/sstmap_test_suite/platforms/amber/gist_output/testcase_Eww-dens.dx /home/debanjan/Downloads/sstmap_test_suite/ref_calcs/gist-Eww-dens.dx
Passed!
/home/debanjan/Downloads/sstmap_test_suite/platforms/amber/gist_output/testcase_dTStrans-dens.dx /home/debanjan/Downloads/sstmap_test_suite/ref_calcs/gist-dTStrans-dens.dx

Arrays are not almost equal to 3 decimals

Mismatch: 1.17%
Max absolute difference: 0.231193
Max relative difference: 65.16527734
x: array([0., 0., 0., ..., 0., 0., 0.])
y: array([0., 0., 0., ..., 0., 0., 0.])
(sstmap) debanjan@debanjan:~/Downloads/sstmap_test_suite$ make test_hsa
cd tests/; python test_platforms_hsa.py
Testing: amber
Initializing ...
Obtaining non-bonded parameters for the system ...
Total time running generate_nonbonded_params: 0.09 seconds
Done.
Assigning hydrogen bond types ...
Total time running assign_hb_types: 0.05 seconds
Done.
Total time running init: 0.20 seconds
System information:
Parameter file: /home/debanjan/Downloads/sstmap_test_suite/platforms/amber/testcase.prmtop

Trajectory: /home/debanjan/Downloads/sstmap_test_suite/platforms/amber/md100ps.nc

Total Atoms: 3026, Waters: 1001, Solute Atoms: 23

Reading trajectory for clustering.
Performing an initial clustering over 10 frames.
Reading trajectory to obtain water molecules for each cluster.
Refining initial cluster positions by considering 100 frames.
Final number of clusters: 25
Total time running generate_clusters: 0.14 seconds
Total time running initialize_site_data: 0.00 seconds
Total time running initialize_hydration_sites: 0.14 seconds
Writing PDB file containing all HSA region water molecules for entropy calculations.
Done.
Writing PDB files for all water molecules in each hydration site.
Done.
Total time running generate_data_for_entropycalcs: 0.06 seconds
Generating expanded cluster water files...
Running entropy calculation from extension module.
double free or corruption (!prev)
Aborted (core dumped)
make: *** [Makefile:5: test_hsa] Error 134

[debanjansen48]

Error in make test_water

(sstmap) debanjan@debanjan:~/Downloads/sstmap_test_suite$ make test_water
cd tests/; python test_water_models.py
Testing: tip3p
Initializing ...
Obtaining non-bonded parameters for the system ...
Total time running generate_nonbonded_params: 0.24 seconds
Done.
Assigning hydrogen bond types ...
Total time running assign_hb_types: 0.01 seconds
Done.
Initializing ...
Total time running init: 0.38 seconds
System information:
Parameter file: /home/debanjan/Downloads/sstmap_test_suite/water_models/tip3p/tip3p.prmtop

Trajectory: /home/debanjan/Downloads/sstmap_test_suite/water_models/tip3p/md100ps.nc

Frames: 100, Total Atoms: 7743, Waters: 2581, Solute Atoms: 0

Grid information:
GIST grid center: 22.506 22.156 21.516

GIST grid dimensions: 20 20 20

GIST grid spacing: 0.500 A^3

Total referenced orientational entropy of the grid: dTSorient = -0.12832 kcal/mol, Nf=100
Total referenced translational entropy of the grid: dTStrans = -0.15166 kcal/mol, Nf=100
Total 6d if all one vox: -0.29620 kcal/mol
Total t if all one vox: -0.00646 kcal/mol
Total o if all one vox: 0.22335 kcal/mol
Total time running calculate_entropy: 0.00 seconds
Total time running calculate_grid_quantities: 3.24 seconds
Writing voxel data ...
Total time running write_data: 0.14 seconds
Summary of main calculations:
Number of frames processed: 100
Average number of water molecules over the grid: 10
Total Solute-Water Energy over the grid: 0.000000
Total Water-Water Energy over the grid: -105.056113
Generating dx files ...
Total time running generate_dx_files: 0.07 seconds
Testing: tip4p
Initializing ...
Obtaining non-bonded parameters for the system ...
Total time running generate_nonbonded_params: 2.28 seconds
Done.
Assigning hydrogen bond types ...
Total time running assign_hb_types: 0.06 seconds
Done.
Initializing ...
Total time running init: 3.19 seconds
System information:
Parameter file: /home/debanjan/Downloads/sstmap_test_suite/water_models/tip4p/tip4p.prmtop

Trajectory: /home/debanjan/Downloads/sstmap_test_suite/water_models/tip4p/md100ps.nc

Frames: 100, Total Atoms: 73244, Waters: 18311, Solute Atoms: 0

Grid information:
GIST grid center: 40.401 40.848 41.257

GIST grid dimensions: 20 20 20

GIST grid spacing: 0.500 A^3

Total referenced orientational entropy of the grid: dTSorient = 1.20519 kcal/mol, Nf=100
Total referenced translational entropy of the grid: dTStrans = -0.24382 kcal/mol, Nf=100
Total 6d if all one vox: -0.13013 kcal/mol
Total t if all one vox: -0.01002 kcal/mol
Total o if all one vox: 0.26619 kcal/mol
Total time running calculate_entropy: 0.02 seconds
Total time running calculate_grid_quantities: 49.78 seconds
Writing voxel data ...
Total time running write_data: 0.80 seconds
Summary of main calculations:
Number of frames processed: 100
Average number of water molecules over the grid: 11
Total Solute-Water Energy over the grid: 0.000000
Total Water-Water Energy over the grid: -109.705456
Generating dx files ...
Total time running generate_dx_files: 0.39 seconds
Testing: tip4pew
Initializing ...
Obtaining non-bonded parameters for the system ...
Segmentation fault (core dumped)
make: *** [Makefile:11: test_water] Error 139

[acruzpr]

Hi, Sorry for the delay, but I was working. There are 2 things that you can try. The first option is to create a new Python environment with python=3.6 and numpy=1.17. Using GCC and GXX v7 and gsl try to install SSTMap again. For the second option, clone the SSTMap repository and check out the *all_conda* branch. Then use sstmap_conda_env.yml to create the conda environment and install SSTMap. These are the changes I recently tested to install SSTMap in an HPC cluster without requiring the installation of additional packages from the system. This should work in any Linux distribution because it uses only resources provided by conda (gcc, gxx, and gsl). Could you try the test suite again after any of the options above? Let me know if this work for you. Regards, Anthony

…

On Mon, Jul 31, 2023 at 3:41 PM debanjansen48 ***@***.***> wrote: *Error in make test_water* (sstmap) ***@***.***:~/Downloads/sstmap_test_suite$ *make test_water* cd tests/; python test_water_models.py Testing: tip3p Initializing ... Obtaining non-bonded parameters for the system ... Total time running generate_nonbonded_params: 0.24 seconds Done. Assigning hydrogen bond types ... Total time running assign_hb_types: 0.01 seconds Done. Initializing ... Total time running *init*: 0.38 seconds System information: Parameter file: /home/debanjan/Downloads/sstmap_test_suite/water_models/tip3p/tip3p.prmtop Trajectory: /home/debanjan/Downloads/sstmap_test_suite/water_models/tip3p/md100ps.nc Frames: 100, Total Atoms: 7743, Waters: 2581, Solute Atoms: 0 Grid information: GIST grid center: 22.506 22.156 21.516 GIST grid dimensions: 20 20 20 GIST grid spacing: 0.500 A^3 Total referenced orientational entropy of the grid: dTSorient = -0.12832 kcal/mol, Nf=100 Total referenced translational entropy of the grid: dTStrans = -0.15166 kcal/mol, Nf=100 Total 6d if all one vox: -0.29620 kcal/mol Total t if all one vox: -0.00646 kcal/mol Total o if all one vox: 0.22335 kcal/mol Total time running calculate_entropy: 0.00 seconds Total time running calculate_grid_quantities: 3.24 seconds Writing voxel data ... Total time running write_data: 0.14 seconds Summary of main calculations: Number of frames processed: 100 Average number of water molecules over the grid: 10 Total Solute-Water Energy over the grid: 0.000000 Total Water-Water Energy over the grid: -105.056113 Generating dx files ... Total time running generate_dx_files: 0.07 seconds Testing: tip4p Initializing ... Obtaining non-bonded parameters for the system ... Total time running generate_nonbonded_params: 2.28 seconds Done. Assigning hydrogen bond types ... Total time running assign_hb_types: 0.06 seconds Done. Initializing ... Total time running *init*: 3.19 seconds System information: Parameter file: /home/debanjan/Downloads/sstmap_test_suite/water_models/tip4p/tip4p.prmtop Trajectory: /home/debanjan/Downloads/sstmap_test_suite/water_models/tip4p/md100ps.nc Frames: 100, Total Atoms: 73244, Waters: 18311, Solute Atoms: 0 Grid information: GIST grid center: 40.401 40.848 41.257 GIST grid dimensions: 20 20 20 GIST grid spacing: 0.500 A^3 Total referenced orientational entropy of the grid: dTSorient = 1.20519 kcal/mol, Nf=100 Total referenced translational entropy of the grid: dTStrans = -0.24382 kcal/mol, Nf=100 Total 6d if all one vox: -0.13013 kcal/mol Total t if all one vox: -0.01002 kcal/mol Total o if all one vox: 0.26619 kcal/mol Total time running calculate_entropy: 0.02 seconds Total time running calculate_grid_quantities: 49.78 seconds Writing voxel data ... Total time running write_data: 0.80 seconds Summary of main calculations: Number of frames processed: 100 Average number of water molecules over the grid: 11 Total Solute-Water Energy over the grid: 0.000000 Total Water-Water Energy over the grid: -109.705456 Generating dx files ... Total time running generate_dx_files: 0.39 seconds Testing: tip4pew Initializing ... Obtaining non-bonded parameters for the system ... Segmentation fault (core dumped) make: *** [Makefile:11: test_water] Error 139 — Reply to this email directly, view it on GitHub <#121 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACLWJSTTWNH7HEBLLO5TSADXTAC6DANCNFSM6AAAAAA26FLYFA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[debanjansen48]

u should not be sorry. I must appreciate your support.Despite of your tremendous work load u extended your hand of support. I am doing that and let you update ASAP. Thanks Sir

[debanjansen48]

sir, from where i will get the sstmap_conda_env.yml file? Its not in the git reposetory. Thanks

[acruzpr]

You need to check out the *all_conda *branch that I created yesterday. *git clone https://github.com/KurtzmanLab/SSTMap.git <https://github.com/KurtzmanLab/SSTMap.git>* then from within the SSTMap repository *git checkout all_conda* Then you will see the file and will have all the changes to use that environment.

…

On Tue, Aug 1, 2023 at 1:35 AM debanjansen48 ***@***.***> wrote: sir, from where i will get the sstmap_conda_env.yml file? Its not in the git reposetory. Thanks — Reply to this email directly, view it on GitHub <#121 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACLWJSV6PVQPVXVMJDJBQY3XTCIT5ANCNFSM6AAAAAA26FLYFA> . You are receiving this because you commented.Message ID: ***@***.***>

[debanjansen48]

(base) debanjan@debanjan:~$ conda create -n sstmap_py36 python=3.6
Retrieving notices: ...working... done
Collecting package metadata (current_repodata.json): done
Solving environment: unsuccessful attempt using repodata from current_repodata.json, retrying with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: done

Package Plan

environment location: /home/debanjan/miniconda3/envs/sstmap_py36

added / updated specs:
- python=3.6

The following NEW packages will be INSTALLED:

_libgcc_mutex pkgs/main/linux-64::_libgcc_mutex-0.1-main
_openmp_mutex pkgs/main/linux-64::_openmp_mutex-5.1-1_gnu
ca-certificates pkgs/main/linux-64::ca-certificates-2023.05.30-h06a4308_0
certifi pkgs/main/linux-64::certifi-2021.5.30-py36h06a4308_0
ld_impl_linux-64 pkgs/main/linux-64::ld_impl_linux-64-2.38-h1181459_1
libffi pkgs/main/linux-64::libffi-3.3-he6710b0_2
libgcc-ng pkgs/main/linux-64::libgcc-ng-11.2.0-h1234567_1
libgomp pkgs/main/linux-64::libgomp-11.2.0-h1234567_1
libstdcxx-ng pkgs/main/linux-64::libstdcxx-ng-11.2.0-h1234567_1
ncurses pkgs/main/linux-64::ncurses-6.4-h6a678d5_0
openssl pkgs/main/linux-64::openssl-1.1.1u-h7f8727e_0
pip pkgs/main/linux-64::pip-21.2.2-py36h06a4308_0
python pkgs/main/linux-64::python-3.6.13-h12debd9_1
readline pkgs/main/linux-64::readline-8.2-h5eee18b_0
setuptools pkgs/main/linux-64::setuptools-58.0.4-py36h06a4308_0
sqlite pkgs/main/linux-64::sqlite-3.41.2-h5eee18b_0
tk pkgs/main/linux-64::tk-8.6.12-h1ccaba5_0
wheel pkgs/main/noarch::wheel-0.37.1-pyhd3eb1b0_0
xz pkgs/main/linux-64::xz-5.4.2-h5eee18b_0
zlib pkgs/main/linux-64::zlib-1.2.13-h5eee18b_0

Proceed ([y]/n)? y

Downloading and Extracting Packages

Preparing transaction: done
Verifying transaction: done
Executing transaction: done

To activate this environment, use

$ conda activate sstmap_py36

To deactivate an active environment, use

$ conda deactivate

(base) debanjan@debanjan:$ source activate sstmap_py36
(sstmap_py36) debanjan@debanjan:$ git clone https://github.com/KurtzmanLab/SSTMap.git
Cloning into 'SSTMap'...
remote: Enumerating objects: 2080, done.
remote: Counting objects: 100% (58/58), done.
remote: Compressing objects: 100% (50/50), done.
remote: Total 2080 (delta 31), reused 16 (delta 8), pack-reused 2022
Receiving objects: 100% (2080/2080), 86.28 MiB | 109.00 KiB/s, done.
Resolving deltas: 100% (1190/1190), done.
(sstmap_py36) debanjan@debanjan:$ git checkout all_conda
fatal: not a git repository (or any of the parent directories): .git
(sstmap_py36) debanjan@debanjan:$

[acruzpr]

You need to be inside the SSTMap directory to check out the branch.
Also, you need to install numpy==1.17

[debanjansen48]

1. Create conda env with py36
2. download / clone from git
3. install numpy 1.17
4. get yml [git checkout all_conda]
5. previously installed gsl and kiwisolver>=1.0.1
6. conda env create --file sstmap_conda_env.yml -n sstmap
7. python setup.py install
   it installed
   now entered the test directory and issue
   1. make test_quick OK
   /home/debanjan/Downloads/sstmap_test_suite/platforms/amber/gist_output/testcase_gO.dx /home/debanjan/Downloads/sstmap_test_suite/ref_calcs/gist-gO.dx
   Passed!
   /home/debanjan/Downloads/sstmap_test_suite/platforms/amber/gist_output/testcase_Eww-dens.dx /home/debanjan/Downloads/sstmap_test_suite/ref_calcs/gist-Eww-dens.dx
   Passed!
   /home/debanjan/Downloads/sstmap_test_suite/platforms/amber/gist_output/testcase_dTStrans-dens.dx /home/debanjan/Downloads/sstmap_test_suite/ref_calcs/gist-dTStrans-dens.dx

Arrays are not almost equal to 3 decimals

Mismatch: 1.17%
Max absolute difference: 0.231193
Max relative difference: 65.16527734
x: array([0., 0., 0., ..., 0., 0., 0.])
y: array([0., 0., 0., ..., 0., 0., 0.])

2. make test_hsa OK
Reading trajectory for clustering.
Performing an initial clustering over 10 frames.
Reading trajectory to obtain water molecules for each cluster.
Refining initial cluster positions by considering 100 frames.
Final number of clusters: 25
Total time running generate_clusters: 0.17 seconds
Total time running initialize_site_data: 0.00 seconds
Total time running initialize_hydration_sites: 0.17 seconds
Writing PDB file containing all HSA region water molecules for entropy calculations.
Done.
Writing PDB files for all water molecules in each hydration site.
Done.
Total time running generate_data_for_entropycalcs: 0.07 seconds
Generating expanded cluster water files...
Running entropy calculation from extension module.
Total time running run_entropy_scripts: 0.03 seconds
Total time running normalize_site_quantities: 0.00 seconds
Total time running calculate_site_quantities: 2.36 seconds
Total time running write_calculation_summary: 0.00 seconds
Total time running write_data: 0.02 seconds

3. make test_gist OK
   Total referenced orientational entropy of the grid: dTSorient = -19.65971 kcal/mol, Nf=100
   Total referenced translational entropy of the grid: dTStrans = -9.66241 kcal/mol, Nf=100
   Total 6d if all one vox: -2.35649 kcal/mol
   Total t if all one vox: -0.55820 kcal/mol
   Total o if all one vox: -0.59395 kcal/mol
   Total time running calculate_entropy: 0.01 seconds
   Total time running calculate_grid_quantities: 2.36 seconds
   Writing voxel data ...
   Total time running write_data: 0.14 seconds
   Summary of main calculations:
   Number of frames processed: 100
   Average number of water molecules over the grid: 15
   Total Solute-Water Energy over the grid: -81.356876
   Total Water-Water Energy over the grid: -116.754827

HOPE NOW IT IS WORKING

One question like to ask you if u consider. Using post processing script let we generate number of dx files. If u guide me how to visualize them in VMD or pymol, how to check, which water clash with my ligand and render the same. It will be helpful.

[debanjansen48]

for my system why it is not working?

(sstmap) debanjan@debanjan:/media/debanjan/DS-1TB/Pradhan-Sir-Student-Bit/Pradhan-Sir-Second-Work/AEQUINETIN/MD/sstmap$ run_hsa -i ../md_100.gro -t ../md_100.xtc -l ../lig.pdb -p ../topol.top -s 0 -f 100 -o testcase
Initializing ...
Obtaining non-bonded parameters for the system ...
Traceback (most recent call last):
File "/home/debanjan/miniconda3/envs/sstmap/bin/run_hsa", line 33, in
sys.exit(load_entry_point('sstmap==1.1.4', 'console_scripts', 'run_hsa')())
File "/home/debanjan/miniconda3/envs/sstmap/lib/python3.6/site-packages/sstmap-1.1.4-py3.6-linux-x86_64.egg/sstmap/scripts/run_hsa.py", line 94, in entry_point
main()
File "/home/debanjan/miniconda3/envs/sstmap/lib/python3.6/site-packages/sstmap-1.1.4-py3.6-linux-x86_64.egg/sstmap/scripts/run_hsa.py", line 84, in main
clustercenter_file=clusters, rho_bulk=args.bulk_density, prefix=args.output_prefix)
File "/home/debanjan/miniconda3/envs/sstmap/lib/python3.6/site-packages/sstmap-1.1.4-py3.6-linux-x86_64.egg/sstmap/utils.py", line 50, in function_timer
result = function(*args, **kwargs)
File "/home/debanjan/miniconda3/envs/sstmap/lib/python3.6/site-packages/sstmap-1.1.4-py3.6-linux-x86_64.egg/sstmap/site_water_analysis.py", line 103, in init
super(SiteWaterAnalysis, self).init(topology_file, trajectory, supporting_file)
File "/home/debanjan/miniconda3/envs/sstmap/lib/python3.6/site-packages/sstmap-1.1.4-py3.6-linux-x86_64.egg/sstmap/water_analysis.py", line 165, in init
self.chg_product, self.acoeff, self.bcoeff = self.generate_nonbonded_params()
File "/home/debanjan/miniconda3/envs/sstmap/lib/python3.6/site-packages/sstmap-1.1.4-py3.6-linux-x86_64.egg/sstmap/utils.py", line 50, in function_timer
result = function(*args, **kwargs)
File "/home/debanjan/miniconda3/envs/sstmap/lib/python3.6/site-packages/sstmap-1.1.4-py3.6-linux-x86_64.egg/sstmap/water_analysis.py", line 344, in generate_nonbonded_params
parmed_topology_object = pmd.load_file(self.supporting_file)
File "/home/debanjan/miniconda3/envs/sstmap/lib/python3.6/site-packages/parmed/formats/registry.py", line 214, in load_file
return cls(filename, *args, **kwargs)
File "/home/debanjan/miniconda3/envs/sstmap/lib/python3.6/site-packages/parmed/gromacs/gromacstop.py", line 251, in init
self.read(fname, defines, parametrize)
File "/home/debanjan/miniconda3/envs/sstmap/lib/python3.6/site-packages/parmed/gromacs/gromacstop.py", line 289, in read
for line in f:
File "/home/debanjan/miniconda3/envs/sstmap/lib/python3.6/site-packages/parmed/gromacs/_gromacsfile.py", line 44, in iter
for line in self._handle:
File "/home/debanjan/miniconda3/envs/sstmap/lib/python3.6/site-packages/parmed/gromacs/_cpp.py", line 175, in iter
self._ppcmdmap[cmd](self, args)
File "/home/debanjan/miniconda3/envs/sstmap/lib/python3.6/site-packages/parmed/gromacs/_cpp.py", line 30, in wrapper
return func(self, args)
File "/home/debanjan/miniconda3/envs/sstmap/lib/python3.6/site-packages/parmed/gromacs/_cpp.py", line 288, in _pp_include
raise PreProcessorError('Could not find %s' % includefile)
(sstmap)

[debanjansen48]

I am able to figured out the issue. Its all about force-field name. Now I am able to run "run_hsa". but it depict following error

(sstmap) debanjan@debanjan:/media/debanjan/DS-1TB/Pradhan-Sir-Student-Bit/Pradhan-Sir-Second-Work/CCL-KN0/gist/GIST$ run_hsa -i ../md_100.gro -t ../md_100.xtc -l ../lig.pdb -p ../topol.top -s 0 -f 100 -o testcase
Initializing ...
Obtaining non-bonded parameters for the system ...
Total time running generate_nonbonded_params: 4.21 seconds
Done.
Assigning hydrogen bond types ...
Total time running assign_hb_types: 0.56 seconds
Done.
Total time running init: 5.05 seconds
Reading trajectory for clustering.
Performing an initial clustering over 10 frames.
Reading trajectory to obtain water molecules for each cluster.
Refining initial cluster positions by considering 100 frames.
Final number of clusters: 0
Total time running generate_clusters: 1.19 seconds
Total time running initialize_site_data: 0.00 seconds
Total time running initialize_hydration_sites: 1.19 seconds
System information:
Parameter file: /media/debanjan/DS-1TB/Pradhan-Sir-Student-Bit/Pradhan-Sir-Second-Work/CCL-KN0/gist/md_100.gro

Trajectory: /media/debanjan/DS-1TB/Pradhan-Sir-Student-Bit/Pradhan-Sir-Second-Work/CCL-KN0/gist/md_100.xtc

Total Atoms: 33941, Waters: 10032, Solute Atoms: 3845

Number of clusters: 0

Writing PDB file containing all HSA region water molecules for entropy calculations.
Done.
Writing PDB files for all water molecules in each hydration site.
Done.
Total time running generate_data_for_entropycalcs: 0.08 seconds
Generating expanded cluster water files...
Segmentation fault (core dumped)

[debanjansen48]

In order to detect the issue as the test suit provided with the software was considered.
inside the gromacs directory i placed my md files and rename accordingly. after execution again getting error. Which means there was some issue with my setup.
(sstmap) debanjan@debanjan:~/Downloads/sstmap_test_suite$ make test_hsa
cd tests/; python test_platforms_hsa.py
Testing: amber
Initializing ...
Obtaining non-bonded parameters for the system ...
Total time running generate_nonbonded_params: 0.11 seconds
Done.
Assigning hydrogen bond types ...
Total time running assign_hb_types: 0.00 seconds
Done.
Total time running init: 0.15 seconds
System information:
Parameter file: /home/debanjan/Downloads/sstmap_test_suite/platforms/amber/testcase.prmtop

Trajectory: /home/debanjan/Downloads/sstmap_test_suite/platforms/amber/md100ps.nc

Total Atoms: 3026, Waters: 1001, Solute Atoms: 23

Reading trajectory for clustering.
Performing an initial clustering over 10 frames.
Reading trajectory to obtain water molecules for each cluster.
Refining initial cluster positions by considering 100 frames.
Final number of clusters: 25
Total time running generate_clusters: 0.13 seconds
Total time running initialize_site_data: 0.00 seconds
Total time running initialize_hydration_sites: 0.13 seconds
Writing PDB file containing all HSA region water molecules for entropy calculations.
Done.
Writing PDB files for all water molecules in each hydration site.
Done.
Total time running generate_data_for_entropycalcs: 0.06 seconds
Generating expanded cluster water files...
Running entropy calculation from extension module.
Total time running run_entropy_scripts: 0.03 seconds
Total time running normalize_site_quantities: 0.00 seconds
Total time running calculate_site_quantities: 2.02 seconds
Total time running write_calculation_summary: 0.00 seconds
Total time running write_data: 0.02 seconds
Testing: charmm
Initializing ...
Obtaining non-bonded parameters for the system ...
/home/debanjan/miniconda3/envs/sstmap/lib/python3.6/site-packages/parmed/charmm/parameters.py:867: UserWarning: WARNING: Ignoring "DELETE ACCE NE2" because entity type ACCE not used.
'used.' % (line.strip(), entity_type))
/home/debanjan/miniconda3/envs/sstmap/lib/python3.6/site-packages/parmed/charmm/parameters.py:747: ParameterWarning: Atom type CC1A not present in AtomType list
warnings.warn('Atom type %s not present in AtomType list' % key, ParameterWarning)
Total time running generate_nonbonded_params: 0.33 seconds
Done.
Assigning hydrogen bond types ...
Total time running assign_hb_types: 0.13 seconds
Done.
Total time running init: 0.75 seconds
System information:
Parameter file: /home/debanjan/Downloads/sstmap_test_suite/platforms/charmm/testcase.psf

Trajectory: /home/debanjan/Downloads/sstmap_test_suite/platforms/charmm/md100ps.dcd

Total Atoms: 7051, Waters: 1940, Solute Atoms: 1231

Reading trajectory for clustering.
Performing an initial clustering over 11 frames.
Reading trajectory to obtain water molecules for each cluster.
Refining initial cluster positions by considering 100 frames.
Final number of clusters: 5
Total time running generate_clusters: 0.34 seconds
Total time running initialize_site_data: 0.00 seconds
Total time running initialize_hydration_sites: 0.34 seconds
Writing PDB file containing all HSA region water molecules for entropy calculations.
Done.
Writing PDB files for all water molecules in each hydration site.
Done.
Total time running generate_data_for_entropycalcs: 0.01 seconds
Generating expanded cluster water files...
Running entropy calculation from extension module.
Total time running run_entropy_scripts: 0.01 seconds
Total time running normalize_site_quantities: 0.00 seconds
Total time running calculate_site_quantities: 1.58 seconds
Total time running write_calculation_summary: 0.00 seconds
Total time running write_data: 0.00 seconds
Testing: desmond
Initializing ...
Obtaining non-bonded parameters for the system ...
Total time running generate_nonbonded_params: 0.01 seconds
Done.
Assigning hydrogen bond types ...
Total time running assign_hb_types: 0.00 seconds
Done.
Total time running init: 0.07 seconds
System information:
Parameter file: /home/debanjan/Downloads/sstmap_test_suite/platforms/desmond/testcase.pdb

Trajectory: /home/debanjan/Downloads/sstmap_test_suite/platforms/desmond/md100ps.nc

Total Atoms: 3026, Waters: 1001, Solute Atoms: 23

Reading trajectory for clustering.
Performing an initial clustering over 10 frames.
Reading trajectory to obtain water molecules for each cluster.
Refining initial cluster positions by considering 100 frames.
Final number of clusters: 25
Total time running generate_clusters: 0.19 seconds
Total time running initialize_site_data: 0.00 seconds
Total time running initialize_hydration_sites: 0.20 seconds
Writing PDB file containing all HSA region water molecules for entropy calculations.
Done.
Writing PDB files for all water molecules in each hydration site.
Done.
Total time running generate_data_for_entropycalcs: 0.06 seconds
Generating expanded cluster water files...
Running entropy calculation from extension module.
Total time running run_entropy_scripts: 0.03 seconds
Total time running normalize_site_quantities: 0.00 seconds
Total time running calculate_site_quantities: 2.08 seconds
Total time running write_calculation_summary: 0.00 seconds
Total time running write_data: 0.02 seconds
Testing: gromacs
Initializing ...
Obtaining non-bonded parameters for the system ...
Total time running generate_nonbonded_params: 4.30 seconds
Done.
Assigning hydrogen bond types ...
Total time running assign_hb_types: 0.64 seconds
Done.
Total time running init: 5.26 seconds
System information:
Parameter file: /home/debanjan/Downloads/sstmap_test_suite/platforms/gromacs/testcase.gro

Trajectory: /home/debanjan/Downloads/sstmap_test_suite/platforms/gromacs/md100ps.xtc

Total Atoms: 33941, Waters: 10032, Solute Atoms: 3845

Reading trajectory for clustering.
Performing an initial clustering over 10 frames.
Reading trajectory to obtain water molecules for each cluster.
Refining initial cluster positions by considering 100 frames.
Final number of clusters: 0
Total time running generate_clusters: 1.45 seconds
Total time running initialize_site_data: 0.00 seconds
Total time running initialize_hydration_sites: 1.45 seconds
Writing PDB file containing all HSA region water molecules for entropy calculations.
Done.
Writing PDB files for all water molecules in each hydration site.
Done.
Total time running generate_data_for_entropycalcs: 0.09 seconds
Generating expanded cluster water files...
Segmentation fault (core dumped)
make: *** [Makefile:5: test_hsa] Error 139
if u guide i will be grateful.

[acruzpr]

Few questions: 1) How long is your simulation? 2) Which water model are you using? 3) What force field are you using? 4) Please, describe your system. What is inside your simulation box? (Nothing specific) 5) Did you use restraints in the protein? 6) Did you visually inspect your systems? The ligand.pdb is in the binding site? 7) What's your background? Chemistry/Biology/Physics? Are you a student? BS/MS/PhD? 8) Have you looked at the posts in sstmap.org 9) Have you read the paper? “Solvation Structure and Thermodynamic Mapping (SSTMap): An Open-Source, Flexible Package for the Analysis of Water in Molecular Dynamics Trajectories” published in the Journal of Chemical Theory and Computation: DOI: 10.1021/acs.jctc.7b00592 <http://pubs.acs.org/doi/10.1021/acs.jctc.7b00592>.

…

On Wed, Aug 2, 2023 at 12:25 PM debanjansen48 ***@***.***> wrote: In order to detect the issue as the test suit provided with the software was considered. inside the gromacs directory i placed my md files and rename accordingly. after execution again getting error. Which means there was some issue with my setup. (sstmap) ***@***.***:~/Downloads/sstmap_test_suite$ make test_hsa cd tests/; python test_platforms_hsa.py Testing: amber Initializing ... Obtaining non-bonded parameters for the system ... Total time running generate_nonbonded_params: 0.11 seconds Done. Assigning hydrogen bond types ... Total time running assign_hb_types: 0.00 seconds Done. Total time running *init*: 0.15 seconds System information: Parameter file: /home/debanjan/Downloads/sstmap_test_suite/platforms/amber/testcase.prmtop Trajectory: /home/debanjan/Downloads/sstmap_test_suite/platforms/amber/md100ps.nc Total Atoms: 3026, Waters: 1001, Solute Atoms: 23 Reading trajectory for clustering. Performing an initial clustering over 10 frames. Reading trajectory to obtain water molecules for each cluster. Refining initial cluster positions by considering 100 frames. Final number of clusters: 25 Total time running generate_clusters: 0.13 seconds Total time running initialize_site_data: 0.00 seconds Total time running initialize_hydration_sites: 0.13 seconds Writing PDB file containing all HSA region water molecules for entropy calculations. Done. Writing PDB files for all water molecules in each hydration site. Done. Total time running generate_data_for_entropycalcs: 0.06 seconds Generating expanded cluster water files... Running entropy calculation from extension module. Total time running run_entropy_scripts: 0.03 seconds Total time running normalize_site_quantities: 0.00 seconds Total time running calculate_site_quantities: 2.02 seconds Total time running write_calculation_summary: 0.00 seconds Total time running write_data: 0.02 seconds Testing: charmm Initializing ... Obtaining non-bonded parameters for the system ... /home/debanjan/miniconda3/envs/sstmap/lib/python3.6/site-packages/parmed/charmm/parameters.py:867: UserWarning: WARNING: Ignoring "DELETE ACCE NE2" because entity type ACCE not used. 'used.' % (line.strip(), entity_type)) /home/debanjan/miniconda3/envs/sstmap/lib/python3.6/site-packages/parmed/charmm/parameters.py:747: ParameterWarning: Atom type CC1A not present in AtomType list warnings.warn('Atom type %s not present in AtomType list' % key, ParameterWarning) Total time running generate_nonbonded_params: 0.33 seconds Done. Assigning hydrogen bond types ... Total time running assign_hb_types: 0.13 seconds Done. Total time running *init*: 0.75 seconds System information: Parameter file: /home/debanjan/Downloads/sstmap_test_suite/platforms/charmm/testcase.psf Trajectory: /home/debanjan/Downloads/sstmap_test_suite/platforms/charmm/md100ps.dcd Total Atoms: 7051, Waters: 1940, Solute Atoms: 1231 Reading trajectory for clustering. Performing an initial clustering over 11 frames. Reading trajectory to obtain water molecules for each cluster. Refining initial cluster positions by considering 100 frames. Final number of clusters: 5 Total time running generate_clusters: 0.34 seconds Total time running initialize_site_data: 0.00 seconds Total time running initialize_hydration_sites: 0.34 seconds Writing PDB file containing all HSA region water molecules for entropy calculations. Done. Writing PDB files for all water molecules in each hydration site. Done. Total time running generate_data_for_entropycalcs: 0.01 seconds Generating expanded cluster water files... Running entropy calculation from extension module. Total time running run_entropy_scripts: 0.01 seconds Total time running normalize_site_quantities: 0.00 seconds Total time running calculate_site_quantities: 1.58 seconds Total time running write_calculation_summary: 0.00 seconds Total time running write_data: 0.00 seconds Testing: desmond Initializing ... Obtaining non-bonded parameters for the system ... Total time running generate_nonbonded_params: 0.01 seconds Done. Assigning hydrogen bond types ... Total time running assign_hb_types: 0.00 seconds Done. Total time running *init*: 0.07 seconds System information: Parameter file: /home/debanjan/Downloads/sstmap_test_suite/platforms/desmond/testcase.pdb Trajectory: /home/debanjan/Downloads/sstmap_test_suite/platforms/desmond/md100ps.nc Total Atoms: 3026, Waters: 1001, Solute Atoms: 23 Reading trajectory for clustering. Performing an initial clustering over 10 frames. Reading trajectory to obtain water molecules for each cluster. Refining initial cluster positions by considering 100 frames. Final number of clusters: 25 Total time running generate_clusters: 0.19 seconds Total time running initialize_site_data: 0.00 seconds Total time running initialize_hydration_sites: 0.20 seconds Writing PDB file containing all HSA region water molecules for entropy calculations. Done. Writing PDB files for all water molecules in each hydration site. Done. Total time running generate_data_for_entropycalcs: 0.06 seconds Generating expanded cluster water files... Running entropy calculation from extension module. Total time running run_entropy_scripts: 0.03 seconds Total time running normalize_site_quantities: 0.00 seconds Total time running calculate_site_quantities: 2.08 seconds Total time running write_calculation_summary: 0.00 seconds Total time running write_data: 0.02 seconds Testing: gromacs Initializing ... Obtaining non-bonded parameters for the system ... Total time running generate_nonbonded_params: 4.30 seconds Done. Assigning hydrogen bond types ... Total time running assign_hb_types: 0.64 seconds Done. Total time running *init*: 5.26 seconds System information: Parameter file: /home/debanjan/Downloads/sstmap_test_suite/platforms/gromacs/testcase.gro Trajectory: /home/debanjan/Downloads/sstmap_test_suite/platforms/gromacs/md100ps.xtc Total Atoms: 33941, Waters: 10032, Solute Atoms: 3845 Reading trajectory for clustering. Performing an initial clustering over 10 frames. Reading trajectory to obtain water molecules for each cluster. Refining initial cluster positions by considering 100 frames. Final number of clusters: 0 Total time running generate_clusters: 1.45 seconds Total time running initialize_site_data: 0.00 seconds Total time running initialize_hydration_sites: 1.45 seconds Writing PDB file containing all HSA region water molecules for entropy calculations. Done. Writing PDB files for all water molecules in each hydration site. Done. Total time running generate_data_for_entropycalcs: 0.09 seconds Generating expanded cluster water files... Segmentation fault (core dumped) make: *** [Makefile:5: test_hsa] Error 139 if u guide i will be grateful. — Reply to this email directly, view it on GitHub <#121 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACLWJSQQGDOMNUIWDO45FELXTJ5P7ANCNFSM6AAAAAA26FLYFA> . You are receiving this because you commented.Message ID: ***@***.***>