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KurtzmanLab / SSTMap

Solvation Structure and Thermodynamic Mapping
MIT License
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Unable to install in LinuxMint #121

Open debanjansen48 opened 1 year ago

debanjansen48 commented 1 year ago

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:

Current channels:

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:

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:

Your installed version is: 2.35**

Please assist me how to resolve the issue.

VjayMolino commented 1 year ago

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 commented 1 year ago

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

debanjansen48 commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

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 https://github.com/KurtzmanLab/SSTMap/issues/121#issuecomment-1659023502, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACLWJSTTWNH7HEBLLO5TSADXTAC6DANCNFSM6AAAAAA26FLYFA . You are receiving this because you are subscribed to this thread.Message ID: @.***>

debanjansen48 commented 1 year ago

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 commented 1 year ago

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

acruzpr commented 1 year ago

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 https://github.com/KurtzmanLab/SSTMap/issues/121#issuecomment-1659597351, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACLWJSV6PVQPVXVMJDJBQY3XTCIT5ANCNFSM6AAAAAA26FLYFA . You are receiving this because you commented.Message ID: @.***>

debanjansen48 commented 1 year ago

(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:

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 commented 1 year ago

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

debanjansen48 commented 1 year ago
  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

  1. 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 commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

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.

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debanjansen48 commented 1 year ago

1) How long is your simulation? ANS: 2ns NVT, 2ns NPT, 100ns Production 2) Which water model are you using? ANS:TIP3P 3) What force field are you using? ANS:CHARMM36 4) Please, describe your system. What is inside your simulation box? (Nothing specific)ANS: 10X10X10 Protein bound with co crystalline ligand, .15M KCL, Water. 5) Did you use restraints in the protein? ANS: No, used CharmmGui input generator, solution bulder to prepare the system. 6) Did you visually inspect your systems? The ligand.pdb is in the binding site? ANS: Yes 7) What's your background? Chemistry/Biology/Physics? Are you a student? BS/MS/PhD? ANS: Organic Medicinal Chemistry (working as an Associate professor). 8) Have you looked at the posts in sstmap.org ANS: Yes I use look around the posts. 9) Have you read the paper? Ans: Studies the abstract as it is not opensource. Unable to get full paper.

We executed MD simulation and the input files were prepared by charmm gui. Then as per the tutorial/usages in sstmap.org we run sstmap.

acruzpr commented 1 year ago

Thanks!

If you visit the Kurtzman lab webpage, you can get the paper. I highly recommend:

  1. Kamran Haider, Lauren Wickstrom, Steven Ramsey, Michael K. Gilson, & Tom Kurtzman. "Enthalpic Breakdown of Water Structure on Protein Active-Site Surfaces" The Journal of Phisical Chemistry Part B (2016)
  2. Kamran Haider, Anthony Cruz, Steven Ramsey, Michael K. Gilson, & Tom Kurtzman. "Solvation Structure and Thermodynamic Mapping (SSTMap): An open-source, flexible package for the analysis of water in molecular dynamics trajectories." Journal of Chemical Theory and Computation (Published November 21, 2017)
  3. Brian Olson, Anthony Cruz, Lieyang Chen, Mossa Ghattas, Yeonji Ji, Kunhui Huang, Steven Ayoub Jr, Tyler Luchko, Daniel J. McKay, Tom Kurtzman. "An online repository of solvation thermodynamic and structural maps of SARS-CoV-2 targets." Journal of Computer-Aided Molecular Design* (Published on August 29, 2020)

The papers explain the simulation protocol for this kind of analysis. Also, you should look at the GIST tutorial on the AMBER website.

You cant use this trajectory to do the analysis. The error you are seeing is likely due to the movement of the protein. You need to apply some restraints to the protein to avoid translations and rotations so that the binding site "stays in place" to analyze the water around it.

Read the papers, redo the trajectory, and try again.

How often are you saving snapshots?

On Thu, Aug 3, 2023 at 1:52 AM debanjansen48 @.***> wrote:

  1. How long is your simulation? ANS: 2ns NVT, 2ns NPT, 100ns Production
  2. Which water model are you using? ANS:TIP3P
  3. What force field are you using? ANS:CHARMM36
  4. Please, describe your system. What is inside your simulation box? (Nothing specific)ANS: Protein bound with co crystaline ligand, .15M KCL, Water.
  5. Did you use restraints in the protein? ANS: No, used CharmmGui input generator, solution bulder to prepare the system.
  6. Did you visually inspect your systems? The ligand.pdb is in the binding site? ANS: Yes
  7. What's your background? Chemistry/Biology/Physics? Are you a student? BS/MS/PhD? ANS: Organic Medicinal Chemistry (working as an Associate professor).
  8. Have you looked at the posts in sstmap.org ANS: Yes I use look arround the posts.
  9. Have you read the paper? Ans: Studies the abstract as it is not opensource. Unable to get full paper.

— Reply to this email directly, view it on GitHub https://github.com/KurtzmanLab/SSTMap/issues/121#issuecomment-1663331128, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACLWJSVVU5GMA37PEI2MJF3XTM4CFANCNFSM6AAAAAA26FLYFA . You are receiving this because you commented.Message ID: @.***>

debanjansen48 commented 1 year ago

2fs. Thanks for your kind reply. I went through Amber GIST tutorial. Now I understand the issue. I need to fiend a solution how to stop the movement of protein in gromacs based simulation.

On Fri, 4 Aug 2023, 6:37 am Anthony Cruz, @.***> wrote:

Thanks!

If you visit the Kurtzman lab webpage, you can get the paper. I highly recommend:

  1. Kamran Haider, Lauren Wickstrom, Steven Ramsey, Michael K. Gilson, & Tom Kurtzman. "Enthalpic Breakdown of Water Structure on Protein Active-Site Surfaces" The Journal of Phisical Chemistry Part B (2016)
  2. Kamran Haider, Anthony Cruz, Steven Ramsey, Michael K. Gilson, & Tom Kurtzman. "Solvation Structure and Thermodynamic Mapping (SSTMap): An open-source, flexible package for the analysis of water in molecular dynamics trajectories." Journal of Chemical Theory and Computation (Published November 21, 2017)
  3. Brian Olson, Anthony Cruz, Lieyang Chen, Mossa Ghattas, Yeonji Ji, Kunhui Huang, Steven Ayoub Jr, Tyler Luchko, Daniel J. McKay, Tom Kurtzman. "An online repository of solvation thermodynamic and structural maps of SARS-CoV-2 targets." Journal of Computer-Aided Molecular Design* (Published on August 29, 2020)

The papers explain the simulation protocol for this kind of analysis. Also, you should look at the GIST tutorial on the AMBER website.

You cant use this trajectory to do the analysis. The error you are seeing is likely due to the movement of the protein. You need to apply some restraints to the protein to avoid translations and rotations so that the binding site "stays in place" to analyze the water around it.

Read the papers, redo the trajectory, and try again.

How often are you saving snapshots?

On Thu, Aug 3, 2023 at 1:52 AM debanjansen48 @.***> wrote:

  1. How long is your simulation? ANS: 2ns NVT, 2ns NPT, 100ns Production
  2. Which water model are you using? ANS:TIP3P
  3. What force field are you using? ANS:CHARMM36
  4. Please, describe your system. What is inside your simulation box? (Nothing specific)ANS: Protein bound with co crystaline ligand, .15M KCL, Water.
  5. Did you use restraints in the protein? ANS: No, used CharmmGui input generator, solution bulder to prepare the system.
  6. Did you visually inspect your systems? The ligand.pdb is in the binding site? ANS: Yes
  7. What's your background? Chemistry/Biology/Physics? Are you a student? BS/MS/PhD? ANS: Organic Medicinal Chemistry (working as an Associate professor).
  8. Have you looked at the posts in sstmap.org ANS: Yes I use look arround the posts.
  9. Have you read the paper? Ans: Studies the abstract as it is not opensource. Unable to get full paper.

— Reply to this email directly, view it on GitHub < https://github.com/KurtzmanLab/SSTMap/issues/121#issuecomment-1663331128>,

or unsubscribe < https://github.com/notifications/unsubscribe-auth/ACLWJSVVU5GMA37PEI2MJF3XTM4CFANCNFSM6AAAAAA26FLYFA>

. You are receiving this because you commented.Message ID: @.***>

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debanjansen48 commented 1 year ago

sir, I may be wrong ! Plz dont mistake me. I explored given articles. I found MD engines are Desmond or Amber. The brief information is I need to restraint protein. Now i wanted to know

  1. Shall I need to restraint only protein? Or both protein and ligand.
  2. In which step a) minimization b) NVT equilibration c) NPT equilibration or d) Production I need to apply restraint
  3. in the Article it was mentioned to use of small simulation box ~531 no of water. Shall I use a grid box only to cover binding site.
  4. In the Amber GIST tutorial they says to execute md for 30+ns... for SSTMAp how long simulation required. certainly my questions are silly ... but as a newbie i am requesting you for assistance. thanks
acruzpr commented 1 year ago

The MD engines are Amber or Desmond, but the principles apply to any MD engine.

  1. Shall I need to restraint only protein? Or both protein and ligand.
    1. It depends on what you are trying to do. What are you trying to do? What information are you expecting to get from this analysis? How are you going to use the information?
    2. In which step a) minimization b) NVT equilibration c) NPT equilibration or d) Production I need to apply restraint
    3. The answer to this question is in the Olson paper that I recommended.
    4. in the Article it was mentioned to use of small simulation box ~531 no of water. Shall I use a grid box only to cover binding site.
    5. The answer to this is in the GIST tutorial and the Olson paper.
    6. In the Amber GIST tutorial they says to execute md for 30+ns... for SSTMAp how long simulation required. certainly my questions are silly ... but as a newbie i am requesting you for assistance. thanks
    7. The requirements for GIST in Amber and SSTMap are the same. Check the Olson paper.

Im not sure how much experience you have with MD or GROMACS but you should try the GROMACS tutorials and look at this https://livecomsjournal.org/index.php/livecoms/article/view/v1i1e5957

—

On Fri, Aug 4, 2023 at 8:05 AM debanjansen48 @.***> wrote:

sir, I may be wrong ! Plz dont mistake me. I explored given articles. I found MD engines are Desmond or Amber. The brief information is I need to restraint protein. Now i wanted to know

  1. Shall I need to restraint only protein? Or both protein and ligand.
  2. In which step a) minimization b) NVT equilibration c) NPT equilibration or d) Production I need to apply restraint
  3. in the Article it was mentioned to use of small simulation box ~531 no of water. Shall I use a grid box only to cover binding site.
  4. In the Amber GIST tutorial they says to execute md for 30+ns... for SSTMAp how long simulation required. certainly my questions are silly ... but as a newbie i am requesting you for assistance. thanks

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debanjansen48 commented 1 year ago

Thanks a lot.

On Fri, Aug 4, 2023 at 7:18 PM Anthony Cruz @.***> wrote:

The MD engines are Amber or Desmond, but the principles apply to any MD engine.

  1. Shall I need to restraint only protein? Or both protein and ligand.
  2. It depends on what you are trying to do. What are you trying to do? What information are you expecting to get from this analysis? How are you going to use the information?
  3. In which step a) minimization b) NVT equilibration c) NPT equilibration or d) Production I need to apply restraint
  4. The answer to this question is in the Olson paper that I recommended.
  5. in the Article it was mentioned to use of small simulation box ~531 no of water. Shall I use a grid box only to cover binding site.
  6. The answer to this is in the GIST tutorial and the Olson paper.
  7. In the Amber GIST tutorial they says to execute md for 30+ns... for SSTMAp how long simulation required. certainly my questions are silly ... but as a newbie i am requesting you for assistance. thanks
  8. The requirements for GIST in Amber and SSTMap are the same. Check the Olson paper.

Im not sure how much experience you have with MD or GROMACS but you should try the GROMACS tutorials and look at this https://livecomsjournal.org/index.php/livecoms/article/view/v1i1e5957

—

On Fri, Aug 4, 2023 at 8:05 AM debanjansen48 @.***> wrote:

sir, I may be wrong ! Plz dont mistake me. I explored given articles. I found MD engines are Desmond or Amber. The brief information is I need to restraint protein. Now i wanted to know

  1. Shall I need to restraint only protein? Or both protein and ligand.
  2. In which step a) minimization b) NVT equilibration c) NPT equilibration or d) Production I need to apply restraint
  3. in the Article it was mentioned to use of small simulation box ~531 no of water. Shall I use a grid box only to cover binding site.
  4. In the Amber GIST tutorial they says to execute md for 30+ns... for SSTMAp how long simulation required. certainly my questions are silly ... but as a newbie i am requesting you for assistance. thanks

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debanjansen48 commented 1 year ago

Appreciate for sharing the link [https://livecomsjournal.org/index.php/livecoms/article/view/v1i1e5957]. It helps me a lot to know more about MD simulation. I am beginner with MD. All I learned from community and you tube. The question is why? On the basis of practical experience I am stating for an organic medicinal chemist its important to know CADD topics a bit. Else after a multi step , expensive organic synthesis the whole event ended up with inactive or less active or molecules can not be taken forward. However, I found some one design such molecules, for them practical synthesis seems to be critical or involves many more steps. In order to synchronism I started the learning process of CADD specially MD. Still I am in the learning process.

Now 1st thing 1st [ref qno 1: What information are you expecting to get from this analysis? How are you going to use the information?] Ans: During docking we remove water. A ligated fit inside the empty pocket depict excellent docking score and conventional MD simulation advocate the binding. But in reality, during in vitro experiment it shows compromised activity profile. May be water play crucial role. In order to analyze approximately the position of stable and replaceable waters and thus any water-ligand clash , water-ligand -protein interactions takes place or not , i want to use sstmap.

acruzpr commented 1 year ago

Thanks for answering my questions.

Then you could find these 2 papers interesting:

Nguyen, Crystal N., Anthony Cruz, Michael K. Gilson, & Tom Kurtzman. "Thermodynamics of Water in an Enzyme Active Site: Grid-Based Hydration Analysis of Coagulation Factor Xa." Journal of Chemical Theory and Computation 10 (2014)

Trent E. Balius, Marcus Fischer, Reed M. Stein, Thomas B. Adler, Crystal N. Nguyen, Anthony Cruz, Michael K. Gilson, Tom Kurtzman, & Brian K. Shoichet. "Testing Inhomogeneous Solvation Theory in Structure-Based Ligand Discovery" Proceedings of the National Academy of Sciences (Published July 31, 2017)

To get the information you want, you should simulate the protein with the empty pocket and another with the ligand bound. That way, you will know how the water was in the pocket when it was empty and how it reorganized in the presence of the ligand.

Are you in academia part-time or full-time?

On Sat, Aug 5, 2023 at 9:45 AM debanjansen48 @.***> wrote:

Appreciate for sharing the link [ https://livecomsjournal.org/index.php/livecoms/article/view/v1i1e5957]. It helps me a lot to know more about MD simulation. I am beginner with MD. All I learned from community and you tube. The question is why? On the basis of practical experience I am stating for an organic medicinal chemist its important to know CADD topics a bit. Else after a multi step , expensive organic synthesis the whole event ended up with inactive or less active or molecules can not be taken forward. However, I found some one design such molecules, for them practical synthesis seems to be critical or involves many more steps. In order to synchronism I started the learning process of CADD specially MD. Still I am in the learning process.

Now st thing 1st [ref qno 1: What information are you expecting to get from this analysis? How are you going to use the information?] Ans: During docking we remove water. A ligated fit inside the empty pocket depict excellent docking score and conventional MD simulation advocate the binding. But in reality, during in vitro experiment it shows compromised activity profile. May be water play crucial role. In order to analyze approximately the position of stable and replaceable waters and thus any water-ligand clash , water-ligand -protein interactions takes place or not , i want to use sstmap.

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debanjansen48 commented 1 year ago

Thanks a lot for sharing. Full time sir.

On Sat, 5 Aug 2023, 8:17 pm Anthony Cruz, @.***> wrote:

Thanks for answering my questions.

Then you could find these 2 papers interesting:

Nguyen, Crystal N., Anthony Cruz, Michael K. Gilson, & Tom Kurtzman. "Thermodynamics of Water in an Enzyme Active Site: Grid-Based Hydration Analysis of Coagulation Factor Xa." Journal of Chemical Theory and Computation 10 (2014)

Trent E. Balius, Marcus Fischer, Reed M. Stein, Thomas B. Adler, Crystal N. Nguyen, Anthony Cruz, Michael K. Gilson, Tom Kurtzman, & Brian K. Shoichet. "Testing Inhomogeneous Solvation Theory in Structure-Based Ligand Discovery" Proceedings of the National Academy of Sciences (Published July 31, 2017)

To get the information you want, you should simulate the protein with the empty pocket and another with the ligand bound. That way, you will know how the water was in the pocket when it was empty and how it reorganized in the presence of the ligand.

Are you in academia part-time or full-time?

On Sat, Aug 5, 2023 at 9:45 AM debanjansen48 @.***> wrote:

Appreciate for sharing the link [ https://livecomsjournal.org/index.php/livecoms/article/view/v1i1e5957]. It helps me a lot to know more about MD simulation. I am beginner with MD. All I learned from community and you tube. The question is why? On the basis of practical experience I am stating for an organic medicinal chemist its important to know CADD topics a bit. Else after a multi step , expensive organic synthesis the whole event ended up with inactive or less active or molecules can not be taken forward. However, I found some one design such molecules, for them practical synthesis seems to be critical or involves many more steps. In order to synchronism I started the learning process of CADD specially MD. Still I am in the learning process.

Now st thing 1st [ref qno 1: What information are you expecting to get from this analysis? How are you going to use the information?] Ans: During docking we remove water. A ligated fit inside the empty pocket depict excellent docking score and conventional MD simulation advocate the binding. But in reality, during in vitro experiment it shows compromised activity profile. May be water play crucial role. In order to analyze approximately the position of stable and replaceable waters and thus any water-ligand clash , water-ligand -protein interactions takes place or not , i want to use sstmap.

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