getting zero values for all of gist's term in output file

[Zahratehrani]

Hi All, I have used "test_platforms_gist.py" on my AMBER-MD results (40ns/.nc and .prmtop files) and in the text output file just voxel and x y z have non-zero values and it prints out zero for other columns so can you please let me know how to fix the issue. Thanks Cheers Zahra

[wutobias]

Hi Zahra, from what you describe I guess the coordinates were not "re-imaged" into the primary simulation cell prior to trajectory processing with GIST. You can achieve the re-imaging by processing the trajectory with the autoimage command from cpptraj first and then feed the resulting trajectory into SSTMap. Alternately, you might already specify iwrap=1 (note, default is iwrap=0) in the input file for sander/pmemd in order to have all coordinates in the primary simulation cell directly after running the simulation. Hope that helps! Tobias

[Zahratehrani]

Dear Tobias, Hi and thanks for your comment. I have used the following script for merging my trajectories: in ccpprtaj so "autoimage" was already included.

!/bin/bash

cd /storage/plzen1/home/zahratehrani7/MD/MD-GIST/merge

module add amber-16-gpu source /software/amber-16/gpu/amber.sh

/software/amber-16/gpu/bin/cpptraj /storage/plzen1/home/zahratehrani7/MD/sdf.top > cpptraj_merge.out << EOF

trajin /storage/plzen1/home/zahratehrani7/STING-MD/MD-GIST/sdf_1_dyn.nc 1 last 1 trajin /storage/plzen1/home/zahratehrani7/STING-MD/MD-GIST/sdf_2_dyn.nc 1 last 1

autoimage strip :Cl-,Na+ outprefix Wat

trajout sdf_Wat_Sup.nc netcd

run

EOF

but I have unwrapped/wrapped or "re-imaged" trajectory file again in VMD as follow :

pbc unwrap -sel "protein or resname SDF" -all pbc wrap -centersel "protein or resname SDF" -center bb -compound residue -all animate write dcd sdf-wrap.dcd

with new .sdf-wrap.dcd file GIST is not working yet. here is some part of GIST output file...

voxel x y z nwat gO dTStr-dens dTStr-norm dTSor-dens dTSor-norm dTSsix-dens dTSsix-norm Esw-dens Esw-norm Eww-dens Eww-norm Eww-nbr-dens Eww-nbr-norm Nnbr-dens Nnbr-norm fHB-dens fHB-norm Nhbsw_dens Nhbsw_norm Nhbww_dens Nhbww_norm Ndonsw_dens Ndonsw_norm Naccsw_dens Naccsw_norm Ndonww_dens Ndonww_norm Naccww_dens Naccww_norm 0 -18.755 5.915 -27.191 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 -18.755 5.915 -26.691 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 -18.755 5.915 -26.191 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 -18.755 5.915 -25.691 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 -18.755 5.915 -25.191 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 -18.755 5.915 -24.691 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

Thanks in advanced Cheers Zahra

[wutobias]

Sorry, I probably missed that, but did you run the gist analysis with sdf_Wat_Sup.nc or with sdf-wrap.dcd? And which one didn't work? I'm just asking in order to exclude any problem with reading the different file formats. You mentioned the "test_platforms_gist.py" script. When initializing the GridWaterAnalysis object (line 30 in the original test_platforms_gist.py script), I assume you provided a file containing a ligand molecule in order to define a gist region? Is this ligand molecule still accommodated in the binding site after re-imaging the trajectory files in cpptraj? If you load the trajectory into vmd together with one of the (I guess empty) dx files generated from sstmap, is the grid located where it should be?

Good luck! Tobias

[acruzpr]

Hi Zahra,

Did you visually inspected the trajectory?

If you are doing some test, just select the first 100 frames from your simulation. This is going to be faster than processing 40ns.

Also, you should use "run_gist" instead of "test_platforms_gist.py".

Regards,

Anthony

On Thu, Aug 29, 2019 at 8:49 AM Zahratehrani notifications@github.com wrote:

Dear Tobias, Hi and thanks for your comment. I have used the following script for merging my trajectories: in ccpprtaj so "autoimage" was already included.

!/bin/bash

cd /storage/plzen1/home/zahratehrani7/MD/MD-GIST/merge

module add amber-16-gpu source /software/amber-16/gpu/amber.sh

/software/amber-16/gpu/bin/cpptraj /storage/plzen1/home/zahratehrani7/MD/sdf.top > cpptraj_merge.out << EOF

trajin /storage/plzen1/home/zahratehrani7/STING-MD/MD-GIST/sdf_1_dyn.nc 1 last 1 trajin /storage/plzen1/home/zahratehrani7/STING-MD/MD-GIST/sdf_2_dyn.nc 1 last 1

autoimage strip :Cl-,Na+ outprefix Wat

trajout sdf_Wat_Sup.nc netcd

run

EOF

but I have unwrapped/wrapped or "re-imaged" trajectory file again in VMD as follow :

pbc unwrap -sel "protein or resname SDF" -all pbc wrap -centersel "protein or resname SDF" -center bb -compound residue -all animate write dcd sdf-wrap.dcd

with new .sdf-wrap.dcd file GIST is not working yet. here is some part of GIST output file...

voxel x y z nwat gO dTStr-dens dTStr-norm dTSor-dens dTSor-norm dTSsix-dens dTSsix-norm Esw-dens Esw-norm Eww-dens Eww-norm Eww-nbr-dens Eww-nbr-norm Nnbr-dens Nnbr-norm fHB-dens fHB-norm Nhbsw_dens Nhbsw_norm Nhbww_dens Nhbww_norm Ndonsw_dens Ndonsw_norm Naccsw_dens Naccsw_norm Ndonww_dens Ndonww_norm Naccww_dens Naccww_norm 0 -18.755 5.915 -27.191 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 -18.755 5.915 -26.691 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 -18.755 5.915 -26.191 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 -18.755 5.915 -25.691 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 -18.755 5.915 -25.191 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 -18.755 5.915 -24.691 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

Thanks in advanced Cheers Zahra

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/KurtzmanLab/SSTMap/issues/100?email_source=notifications&email_token=ACLWJSRKSORGDFVXTO4OZCDQG7AUVA5CNFSM4IR7APSKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD5OLMBA#issuecomment-526169604, or mute the thread https://github.com/notifications/unsubscribe-auth/ACLWJSUJPAR62MZEOP3PTA3QG7AUVANCNFSM4IR7APSA .

[Zahratehrani]

Dear Tobias/ Dear Anthony, Hi again.. I have used ligand.pdb (taken from x-ray pdb) .top and .dcd file and have updated the test_platforms_gist.py.py as : import sys import os import shutil from sstmap.grid_water_analysis import GridWaterAnalysis platforms = ["amber"] top_ext = [".prmtop",".pdb"] trj_ext = [".dcd"] supp_ext = [None, "toppar", "params.txt", "params.top", "toppar", None] curr_dir = os.getcwd()

for index, platform in enumerate(platforms): print("Testing: %s" % platform) data_dir = os.path.abspath("../platforms/" + platform + "/gist_output") if not os.path.exists(data_dir): os.makedirs(data_dir) else: shutil.rmtree(data_dir) #removes all the subdirectories! os.makedirs(data_dir) top = os.path.abspath("../platforms/" + platform + "/" + "sting" + top_ext[index]) traj = os.path.abspath("../platforms/" + platform + "/" + "sting" + trj_ext[index]) supp = None if supp_ext[index] is not None: supp = os.path.abspath("../platforms/" + platform + "/" + supp_ext[index]) ligand = os.path.abspath("../platforms/" + platform + "/" + "ligand.pdb") s = 0 n = 4000 os.chdir(data_dir) gist = GridWaterAnalysis(top, traj, start_frame=s, num_frames=n, ligand_file=ligand, supporting_file=supp, grid_dimensions=[40.0, 40.0, 40.0], prefix="sting") gist.print_system_summary() gist.calculate_grid_quantities(hbonds=True) gist.write_data() gist.print_calcs_summary() os.chdir(curr_dir)

here is ouput file and I did not get any .dx file to test but GIST grid center/dimension parameters are the same as I got from Autodock tools. I have checked also the complied SSTMap on my system there is no "run_gist" and just quick_test.py, test_platforms_gist.py, test_platforms_hsa.py, test_platforms_org_gist.py and test_water_models.py are available there... python test_platforms_gist.py Testing: amber Initializing ... Obtaining non-bonded parameters for the system ... Total time running generate_nonbonded_params: 7.65 seconds Done. Assigning hydrogen bond types ... Total time running assign_hb_types: 4.72 seconds Done. Initializing ... Total time running init: 16.32 seconds System information: Parameter file: /auto/plzen1/home/zahratehrani7/STING-MD/GIST-test/platforms/amber/sting.prmtop

    Trajectory: /auto/plzen1/home/zahratehrani7/STING-MD/GIST-test/platforms/amber/sting.dcd

    Frames: 4000, Total Atoms: 72376, Waters: 22143, Solute Atoms: 5947

Grid information: GIST grid center: -9.005 15.665 -17.441

    GIST grid dimensions: 40 40 40

    GIST grid spacing: 0.500 A^3

Total referenced orientational entropy of the grid: dTSorient = 0.00000 kcal/mol, Nf=4000 Total referenced translational entropy of the grid: dTStrans = 0.00000 kcal/mol, Nf=4000 Total 6d if all one vox: 0.00000 kcal/mol Total t if all one vox: 0.00000 kcal/mol Total o if all one vox: -nan kcal/mol Total time running calculate_entropy: 0.00 seconds Total time running calculate_grid_quantities: 106.58 seconds Writing voxel data ... Total time running write_data: 2.34 seconds Summary of main calculations: Number of frames processed: 4000 Average number of water molecules over the grid: 0 Total Solute-Water Energy over the grid: 0.000000 Total Water-Water Energy over the grid: 0.000000

Thanks Zahra

[acruzpr]

Hi Zahra,

How do you installed SSTMap?

Did you use the conda package or compile it from the git repository?

"run_gist" is a script that is installed with SSTMap and you should be able to use it by typing "run_gist" in the terminal. Without any options, it will show you its usage.

Also, depending on the type of trajectory SSTMap will need the parm.txt helper file. If you dont provide this file you could get all zeros.

Regards,

Anthony

On Thu, Aug 29, 2019 at 10:31 AM Zahratehrani notifications@github.com wrote:

Dear Tobias/ Dear Anthony, Hi again.. I have used ligand.pdb (taken from x-ray pdb) .top and .dcd file and have updated the test_platforms_gist.py.py as : import sys import os import shutil from sstmap.grid_water_analysis import GridWaterAnalysis platforms = ["amber"] top_ext = [".prmtop",".pdb"] trj_ext = [".dcd"] supp_ext = [None, "toppar", "params.txt", "params.top", "toppar", None] curr_dir = os.getcwd()

for index, platform in enumerate(platforms): print("Testing: %s" % platform) data_dir = os.path.abspath("../platforms/" + platform + "/gist_output") if not os.path.exists(data_dir): os.makedirs(data_dir) else: shutil.rmtree(data_dir) #removes all the subdirectories! os.makedirs(data_dir) top = os.path.abspath("../platforms/" + platform + "/" + "sting" + top_ext[index]) traj = os.path.abspath("../platforms/" + platform + "/" + "sting" + trj_ext[index]) supp = None if supp_ext[index] is not None: supp = os.path.abspath("../platforms/" + platform + "/" + supp_ext[index]) ligand = os.path.abspath("../platforms/" + platform + "/" + "ligand.pdb") s = 0 n = 4000 os.chdir(data_dir) gist = GridWaterAnalysis(top, traj, start_frame=s, num_frames=n, ligand_file=ligand, supporting_file=supp, grid_dimensions=[40.0, 40.0, 40.0], prefix="sting") gist.print_system_summary() gist.calculate_grid_quantities(hbonds=True) gist.write_data() gist.print_calcs_summary() os.chdir(curr_dir)

here is ouput file and I did not get any .dx file to test but GIST grid center/dimension parameters are the same as I got from Autodock tools. I have checked also the complied SSTMap on my system there is no "run_gist" and just quick_test.py, test_platforms_gist.py, test_platforms_hsa.py, test_platforms_org_gist.py and test_water_models.py are available there... python test_platforms_gist.py Testing: amber Initializing ... Obtaining non-bonded parameters for the system ... Total time running generate_nonbonded_params: 7.65 seconds Done. Assigning hydrogen bond types ... Total time running assign_hb_types: 4.72 seconds Done. Initializing ... Total time running init: 16.32 seconds System information: Parameter file: /auto/plzen1/home/zahratehrani7/STING-MD/GIST-test/platforms/amber/sting.prmtop

Trajectory: /auto/plzen1/home/zahratehrani7/STING-MD/GIST-test/platforms/amber/sting.dcd

Frames: 4000, Total Atoms: 72376, Waters: 22143, Solute Atoms: 5947

Grid information: GIST grid center: -9.005 15.665 -17.441

GIST grid dimensions: 40 40 40

GIST grid spacing: 0.500 A^3

Total referenced orientational entropy of the grid: dTSorient = 0.00000 kcal/mol, Nf=4000 Total referenced translational entropy of the grid: dTStrans = 0.00000 kcal/mol, Nf=4000 Total 6d if all one vox: 0.00000 kcal/mol Total t if all one vox: 0.00000 kcal/mol Total o if all one vox: -nan kcal/mol Total time running calculate_entropy: 0.00 seconds Total time running calculate_grid_quantities: 106.58 seconds Writing voxel data ... Total time running write_data: 2.34 seconds Summary of main calculations: Number of frames processed: 4000 Average number of water molecules over the grid: 0 Total Solute-Water Energy over the grid: 0.000000 Total Water-Water Energy over the grid: 0.000000

Thanks Zahra

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/KurtzmanLab/SSTMap/issues/100?email_source=notifications&email_token=ACLWJSWEGTDDJ5R6FFUXCC3QG7MSXA5CNFSM4IR7APSKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD5OV5DA#issuecomment-526212748, or mute the thread https://github.com/notifications/unsubscribe-auth/ACLWJSU3T5IIG7UCDU2IW6TQG7MSXANCNFSM4IR7APSA .

[Zahratehrani]

Dear Anthony, done with Python because compilation by using conda was not available on the machine ...will try to recompil it ... Cheers Zahra

[Zahratehrani]

Hi all, sorry for late reply.. was in conferences … so I have recompiled it with mini-conda its fine for testcase but still has problem with my system and seems the clustring can not be done and (Final number of clusters: 0) got Segmentation fault (core dumped) at the end...any suggestion will be appreciated: Cheers Zahra testcase result:

(base) (STRETCH)zahratehrani7@skirit:/storage/plzen1/home/zahratehrani7/STING-MD/GIST-test/2-3-GAMP/test-5$ run_hsa -i testcase.prmtop -t testcase.nc -l ligand.pdb -s 0 -f 100 -o testcase Initializing ... Obtaining non-bonded parameters for the system ... Total time running generate_nonbonded_params: 0.25 seconds Done. Assigning hydrogen bond types ... Total time running assign_hb_types: 0.02 seconds Done. Total time running init: 0.44 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: 25 Total time running generate_clusters: 0.40 seconds Total time running initialize_site_data: 0.00 seconds Total time running initialize_hydration_sites: 0.40 seconds System information: Parameter file: /auto/plzen1/home/zahratehrani7/STING-MD/GIST-test/2-3-GAMP/test-5/testcase.prmtop

    Trajectory: /auto/plzen1/home/zahratehrani7/STING-MD/GIST-test/2-3-GAMP/test-5/testcase.nc

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

    Number of clusters: 25

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: 2.49 seconds Generating expanded cluster water files... Running entropy calculation from extension module. Total time running run_entropy_scripts: 5.68 seconds Total time running normalize_site_quantities: 0.02 seconds Total time running calculate_site_quantities: 12.02 seconds Total time running write_calculation_summary: 0.02 seconds Total time running write_data: 14.30 seconds

my model result: Initializing ... Obtaining non-bonded parameters for the system ... Total time running generate_nonbonded_params: 7.19 seconds Done. Assigning hydrogen bond types ... Total time running assign_hb_types: 4.63 seconds Done. Total time running init: 14.77 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: 12.09 seconds Total time running initialize_site_data: 0.00 seconds Total time running initialize_hydration_sites: 12.09 seconds System information: Parameter file: /auto/plzen1/home/zahratehrani7/STING-MD/GIST-test/2-3-GAMP/test-4/sting.prmtop

    Trajectory: /auto/plzen1/home/zahratehrani7/STING-MD/GIST-test/2-3-GAMP/test-4/sting.nc

    Total Atoms: 72376, Waters: 22143, Solute Atoms: 5947

    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: 0.29 seconds Generating expanded cluster water files... Segmentation fault (core dumped)

[tkurtzman]

Zahra, did you visually inspect your trajectory as Anthony asked?

1) Is the analysis region (ligand) in the box 2) Is the protein/solute restrained and staying in the center of the box?

Tom

On Sun, Sep 8, 2019 at 7:49 AM Zahratehrani notifications@github.com wrote:

Hi all, sorry for late reply.. was in conferences … so I have recompiled it with mini-conda its fine for testcase but still has problem with my system and seems the clustring can not be done and (Final number of clusters: 0) got Segmentation fault (core dumped) at the end...any suggestion will be appreciated: Cheers Zahra testcase result:

(base) (STRETCH)zahratehrani7@skirit:/storage/plzen1/home/zahratehrani7/STING-MD/GIST-test/2-3-GAMP/test-5$ run_hsa -i testcase.prmtop -t testcase.nc -l ligand.pdb -s 0 -f 100 -o testcase Initializing ... Obtaining non-bonded parameters for the system ... Total time running generate_nonbonded_params: 0.25 seconds Done. Assigning hydrogen bond types ... Total time running assign_hb_types: 0.02 seconds Done. Total time running init: 0.44 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: 25 Total time running generate_clusters: 0.40 seconds Total time running initialize_site_data: 0.00 seconds Total time running initialize_hydration_sites: 0.40 seconds System information: Parameter file: /auto/plzen1/home/zahratehrani7/STING-MD/GIST-test/2-3-GAMP/test-5/testcase.prmtop

Trajectory: /auto/plzen1/home/zahratehrani7/STING-MD/GIST-test/2-3-GAMP/test-5/testcase.nc

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

Number of clusters: 25

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: 2.49 seconds Generating expanded cluster water files... Running entropy calculation from extension module. Total time running run_entropy_scripts: 5.68 seconds Total time running normalize_site_quantities: 0.02 seconds Total time running calculate_site_quantities: 12.02 seconds Total time running write_calculation_summary: 0.02 seconds Total time running write_data: 14.30 seconds

my model result: Initializing ... Obtaining non-bonded parameters for the system ... Total time running generate_nonbonded_params: 7.19 seconds Done. Assigning hydrogen bond types ... Total time running assign_hb_types: 4.63 seconds Done. Total time running init: 14.77 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: 12.09 seconds Total time running initialize_site_data: 0.00 seconds Total time running initialize_hydration_sites: 12.09 seconds System information: Parameter file: /auto/plzen1/home/zahratehrani7/STING-MD/GIST-test/2-3-GAMP/test-4/sting.prmtop

Trajectory: /auto/plzen1/home/zahratehrani7/STING-MD/GIST-test/2-3-GAMP/test-4/sting.nc

Total Atoms: 72376, Waters: 22143, Solute Atoms: 5947

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: 0.29 seconds Generating expanded cluster water files... Segmentation fault (core dumped)

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/KurtzmanLab/SSTMap/issues/100?email_source=notifications&email_token=AGYKFQ5AXG3WEDV7GNKLEVTQITRCZA5CNFSM4IR7APSKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6FOB2I#issuecomment-529195241, or mute the thread https://github.com/notifications/unsubscribe-auth/AGYKFQYRJCWOGMFJI6DCCOTQITRCZANCNFSM4IR7APSA .

--

---

Tom Kurtzman, Ph.D. Associate Professor Department of Chemistry Lehman College, CUNY 250 Bedford Park Blvd. West Bronx, New York 10468 718-960-8832 http://www.lehman.edu/faculty/tkurtzman/ http://www.lehman.edu/faculty/tkurtzman/index.html

---

[acruzpr]

Hi Zahra,

Could be possible for you to share a trajectory of your system with only 100 frames, the prmtop, and the ligand.pdb so we can debug and find out the source of the error?

Best,

Anthony

On Sun, Sep 8, 2019 at 7:49 AM Zahratehrani notifications@github.com wrote:

Hi all, sorry for late reply.. was in conferences … so I have recompiled it with mini-conda its fine for testcase but still has problem with my system and seems the clustring can not be done and (Final number of clusters: 0) got Segmentation fault (core dumped) at the end...any suggestion will be appreciated: Cheers Zahra testcase result:

(base) (STRETCH)zahratehrani7@skirit:/storage/plzen1/home/zahratehrani7/STING-MD/GIST-test/2-3-GAMP/test-5$ run_hsa -i testcase.prmtop -t testcase.nc -l ligand.pdb -s 0 -f 100 -o testcase Initializing ... Obtaining non-bonded parameters for the system ... Total time running generate_nonbonded_params: 0.25 seconds Done. Assigning hydrogen bond types ... Total time running assign_hb_types: 0.02 seconds Done. Total time running init: 0.44 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: 25 Total time running generate_clusters: 0.40 seconds Total time running initialize_site_data: 0.00 seconds Total time running initialize_hydration_sites: 0.40 seconds System information: Parameter file: /auto/plzen1/home/zahratehrani7/STING-MD/GIST-test/2-3-GAMP/test-5/testcase.prmtop

Trajectory: /auto/plzen1/home/zahratehrani7/STING-MD/GIST-test/2-3-GAMP/test-5/testcase.nc

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

Number of clusters: 25

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: 2.49 seconds Generating expanded cluster water files... Running entropy calculation from extension module. Total time running run_entropy_scripts: 5.68 seconds Total time running normalize_site_quantities: 0.02 seconds Total time running calculate_site_quantities: 12.02 seconds Total time running write_calculation_summary: 0.02 seconds Total time running write_data: 14.30 seconds

my model result: Initializing ... Obtaining non-bonded parameters for the system ... Total time running generate_nonbonded_params: 7.19 seconds Done. Assigning hydrogen bond types ... Total time running assign_hb_types: 4.63 seconds Done. Total time running init: 14.77 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: 12.09 seconds Total time running initialize_site_data: 0.00 seconds Total time running initialize_hydration_sites: 12.09 seconds System information: Parameter file: /auto/plzen1/home/zahratehrani7/STING-MD/GIST-test/2-3-GAMP/test-4/sting.prmtop

Trajectory: /auto/plzen1/home/zahratehrani7/STING-MD/GIST-test/2-3-GAMP/test-4/sting.nc

Total Atoms: 72376, Waters: 22143, Solute Atoms: 5947

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: 0.29 seconds Generating expanded cluster water files... Segmentation fault (core dumped)

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/KurtzmanLab/SSTMap/issues/100?email_source=notifications&email_token=ACLWJSX4EHSEZRSTQBAF4I3QITRCXA5CNFSM4IR7APSKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6FOB2I#issuecomment-529195241, or mute the thread https://github.com/notifications/unsubscribe-auth/ACLWJSQC5BK6LBWROMBPZTTQITRCXANCNFSM4IR7APSA .

[Zahratehrani]

Hi all, thanks for suggestion.. I am trying another set of MD with bigger force. have used commands as suggested here in production step : http://ambermd.org/tutorials/advanced/tutorial25/section2.htm restraintmask = ':1-368 & !@H=', restraint_wt = 50.0 (ressidue 369 is the ligand) but protein is not fully rigid.. will post update here once I get it... Thanks in advacned... Cheers Zahra

[acruzpr]

Hi Zahra,

I don't think that the forces are the problem because we use forces of 2.5 without problems.

I think that the problem is that you are not restraining the ligand (residue 369). if your ligand is in your simulation you need to restrain it, you need to restrain all molecules in your system, except the water.

Also, add the ions (to neutralize your system) far from the active site because the ions are known to cause artifacts with the HSA or GIST calculation. The ions cause high-density water sites due to the interaction of water with the ions. These type of sites are false positive that will not exist in other cases where the ions are not present and they could mislead your interpretation of the results.

Regards,

Anthony

On Mon, Sep 9, 2019 at 5:12 AM Zahratehrani notifications@github.com wrote:

Hi all, thanks for suggestion.. I am trying another set of MD with bigger force. have used commands as suggested here in production step : http://ambermd.org/tutorials/advanced/tutorial25/section2.htm restraintmask = ':1-368 & !@h https://github.com/h=', restraint_wt = 50.0 (ressidue 369 is the ligand) but protein is not fully rigid.. will post update here once I get it... Thanks in advacned... Cheers Zahra

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/KurtzmanLab/SSTMap/issues/100?email_source=notifications&email_token=ACLWJSVMHIA7E7YCL74B3PTQIYHRBA5CNFSM4IR7APSKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6GZ62I#issuecomment-529375081, or mute the thread https://github.com/notifications/unsubscribe-auth/ACLWJSWWRWCJH2FJYGWVAHDQIYHRBANCNFSM4IR7APSA .

[Zahratehrani]

Hi Anthony, thanks for our comment.. I was following the AMBER example (as mentioned above) it was about only protein with no ligand but its highly restrain and just H and waters are allowed to relaxed.. so I will repeat all steps means min/heat/eq and production just applying forces to waters and ions .. will post update .. Cheers Zahra

[acruzpr]

Hi Zahra,

In that case, just made sure that after you finish your simulation you align the ligand into the binding site again. To verify that the ligand is aligned with your protein, load the ligand and the restart file from your production run into vmd. Most of the time the ligand will be outside of the binding site because when you prepare your system with (x/t)leap the protein will be moved to the center of the simulation box. Due to this, the ligand is not going to be aligned with the protein anymore.

Regards,

Anthony

On Mon, Sep 9, 2019 at 12:40 PM Zahratehrani notifications@github.com wrote:

Hi Anthony, thanks for our comment.. I was following the AMBER example (as mentioned above) it was about only protein with no ligand but its highly restrain and just H and waters are allowed to relaxed.. so I will repeat all steps means min/heat/eq and production just applying forces to waters and ions .. will post update .. Cheers Zahra

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/KurtzmanLab/SSTMap/issues/100?email_source=notifications&email_token=ACLWJSTRY5QBDMWSWQK6DP3QIZ4AFA5CNFSM4IR7APSKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6IIIII#issuecomment-529564705, or mute the thread https://github.com/notifications/unsubscribe-auth/ACLWJSVP7T642HQZRTGTVU3QIZ4AFANCNFSM4IR7APSA .

[Zahratehrani]

Hi all, I have repeated MD calc for 20 ns to test the hsa.. protein/ligand system is still moving! have used these commands for dynamic and pre-dynamic steps (protein res: 1-368 and ligand is 369). might be better to share some data but even for 100 frames, they are big and don't know how to share them... Thanks in advanced Cheers Zahra

predynamic step:

&cntrl imin=0, irest=1, ntx=5, ntc=2,ntf=2, dt=0.002, nstlim=80000, cut = 9.0, ntb=2, ntp=1, ntpr=1000, ntt=1, taup = 1.0, temp0=300.0, pres0 = 1.0 ntwv=0, ntwe=1000, ntwx=5000,ntwr=10000, ntr=1,ibelly=0, restraintmask=':1-369' restraint_wt=5.0, &end

dynamic:

&cntrl imin=0, irest=1, ntx=5, ntc=2,ntf=2, dt=0.002, cut = 9.0, iwrap=1, nstlim=10000000, ntpr=100000, ntb=1, ntp=0, ntt=3, gamma_ln=3.0,ig=-1, temp0=300.0, ntwv=0, ntwe=0, ntwx=5000,ntwr=10000, ntr=0, restraintmask=':1-369' restraint_wt = 5.0, &end

[wutobias]

Hi Zahra,

in the input file of the production run (your second run) ntr is set to 0, which effectively turns off the positional restraints. For HSA/GIST analysis one would need to turn them on, that is "ntr=1" (as you did correctly in the "pre-dynamics" run). This likely explains your results and the movements of the protein...

I think a good start is to use exactly the procedure as outlined in the GIST tutorial on the amber website: http://ambermd.org/tutorials/advanced/tutorial25/ As Anthony said, it is ok to use a lower force constant then in the tutorial, but everything else should be more or less identical. Of course, if it is applicable to your system.

Regards, Tobias

[Zahratehrani]

Dear Tobias, Hi.. So many thanks,, it was my mistake! I have done couple of MDs on these system in which the system is free to move and then took files from that MDs and made mistake to change it.. sorry for technical problem and hope this time it works fine! Cheers Zahra

[wutobias]

Hi Zahra, good that we identified the issue. Glad to be of help here!

Regards, Tobias

[Zahratehrani]

Hi All, I have tested run_gist and also cpptraj_gist (based on AMBER tutorial with new constraint-MD simulation we discussed here) and still have zero values in .dx files. Water box looks stable and ligand is in x-ray position. Could not figure out the problem so I am sharing .top, .nc (for first 100 frames out of 2000) sdf_leap (solvated protein-ligand complex obtained from tleap) and ligand.pdb file of my system. .nc file is about 77 mb and can not share it here. so have shared it from my G-drive if you can get it here... Any help/suggestion would be appreciated. Cheers https://drive.google.com/file/d/1tfp2GnDubDKoKZIusFMP9bV9CkeN3tFd/view?usp=sharing Wat.sdf.zip sdf_leap.zip

[acruzpr]

Hi Zahra,

I think that the problem is the naming convention that you used for your files. SSTMAP expect an AMBER topology with an extension prmtop but your topology has an extension top. SSTMap thinks that your system was created by other MD package and not by AMBER and is expecting the supporting file with all the LJ parameters. By changing the topology name to Wat.sdf.prmtop I was able to generate come results. Please, try changing the name of your topology.

Regards,

Anthony

On Mon, Sep 16, 2019 at 10:27 AM Zahratehrani notifications@github.com wrote:

Hi All, I have tested run_gist and also cpptraj_gist (based on AMBER tutorial with new constraint-MD simulation we discussed here) and still have zero values in .dx files. Water box looks stable and ligand is in x-ray position. Could not figure out the problem so I am sharing .top, .nc (for first 100 frames out of 2000) sdf_leap (solvated protein-ligand complex obtained from tleap) and ligand.pdb file of my system. .nc file is about 77 mb and can not share it here. so have shared it from my G-drive if you can get it here... Any help/suggestion would be appreciated. Cheers

https://drive.google.com/file/d/1tfp2GnDubDKoKZIusFMP9bV9CkeN3tFd/view?usp=sharing Wat.sdf.zip https://github.com/KurtzmanLab/SSTMap/files/3616677/Wat.sdf.zip sdf_leap.zip https://github.com/KurtzmanLab/SSTMap/files/3616679/sdf_leap.zip

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/KurtzmanLab/SSTMap/issues/100?email_source=notifications&email_token=ACLWJSWOWAFQURUHKXRDPYLQJ6JV3A5CNFSM4IR7APSKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6ZKSEI#issuecomment-531802385, or mute the thread https://github.com/notifications/unsubscribe-auth/ACLWJSXA6NJI67CUFTCLXX3QJ6JV3ANCNFSM4IR7APSA .

[Zahratehrani]

Dear Anthony, Hi.. thanks for your suggestion.... I have changed the extension to .prmtop by making a copy of .top file and test run_hsa and cpptraj in AMBER with files I shared with you. so for run_has, as it was compiled with mini-conda, first I have activated that by: source $HOME/miniconda2/bin/activate then used the following command: run_hsa -i Wat.sdf.prmtop -t sdf-100-frames.nc -l ligand.pdb -s 0 -f 100 -o sdf

Initializing ... Obtaining non-bonded parameters for the system ... Total time running generate_nonbonded_params: 7.56 seconds Done. Assigning hydrogen bond types ... Total time running assign_hb_types: 4.58 seconds Done. Total time running init: 14.67 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: 10.17 seconds Total time running initialize_site_data: 0.00 seconds Total time running initialize_hydration_sites: 10.17 seconds System information: Parameter file: /auto/plzen1/home/zahratehrani7/STING-MD/GIST-test/2-3-GAMP/test-8/test/Wat.sdf.prmtop

    Trajectory: /auto/plzen1/home/zahratehrani7/STING-MD/GIST-test/2-3-GAMP/test-8/test/sdf-100-frames.nc

    Total Atoms: 72376, Waters: 22143, Solute Atoms: 5947

    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: 0.33 seconds Generating expanded cluster water files... Segmentation fault (core dumped)

may be I have to recompile it again but it works fine with "testcase" example (prmtop and nc files). in the second test by using cpptraj in AMBER, got all of .dx files but all values are zero! you can find all of inps/outs for both methods in the attachment.

Thanks in advanced Bests Zahra

SSTMap_HSA.zip CPPTRAJ.zip

[acruzpr]

Hi Zahra,

I think that 100 frame is not enough to test HSA due to the secluded region where the ligand is located. Could you try run_gist? I did my test with GIST.

Regards,

Anthony

On Tue, Sep 17, 2019 at 5:36 AM Zahratehrani notifications@github.com wrote:

Dear Anthony, Hi.. thanks for your suggestion.... I have changed the extension to .prmtop by making a copy of .top file and test run_hsa and cpptraj in AMBER with files I shared with you. so for run_has, as it was compiled with mini-conda, first I have activated that by: source $HOME/miniconda2/bin/activate then used the following command: run_hsa -i Wat.sdf.prmtop -t sdf-100-frames.nc -l ligand.pdb -s 0 -f 100 -o sdf

Initializing ... Obtaining non-bonded parameters for the system ... Total time running generate_nonbonded_params: 7.56 seconds Done. Assigning hydrogen bond types ... Total time running assign_hb_types: 4.58 seconds Done. Total time running init: 14.67 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: 10.17 seconds Total time running initialize_site_data: 0.00 seconds Total time running initialize_hydration_sites: 10.17 seconds System information: Parameter file: /auto/plzen1/home/zahratehrani7/STING-MD/GIST-test/2-3-GAMP/test-8/test/Wat.sdf.prmtop

Trajectory: /auto/plzen1/home/zahratehrani7/STING-MD/GIST-test/2-3-GAMP/test-8/test/sdf-100-frames.nc

Total Atoms: 72376, Waters: 22143, Solute Atoms: 5947

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: 0.33 seconds Generating expanded cluster water files... Segmentation fault (core dumped)

may be I have to recompile it again but it works fine with "testcase" example (prmtop and nc files). in the second test by using cpptraj in AMBER, got all of .dx files but all values are zero! you can find all of inps/outs for both methods in the attachment.

Thanks in advanced Bests Zahra

SSTMap_HSA.zip https://github.com/KurtzmanLab/SSTMap/files/3620440/SSTMap_HSA.zip CPPTRAJ.zip https://github.com/KurtzmanLab/SSTMap/files/3620441/CPPTRAJ.zip

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/KurtzmanLab/SSTMap/issues/100?email_source=notifications&email_token=ACLWJSU442J2UT3WZZSIAEDQKCQKHA5CNFSM4IR7APSKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6355FY#issuecomment-532143767, or mute the thread https://github.com/notifications/unsubscribe-auth/ACLWJSTJPKZEZWVZOR2XU53QKCQKHANCNFSM4IR7APSA .

[tkurtzman]

I recall that there was a minimum of 1000 frames for the HSA though I haven't verified.

On Tue, Sep 17, 2019 at 3:12 PM Anthony Cruz notifications@github.com wrote:

Hi Zahra,

I think that 100 frame is not enough to test HSA due to the secluded region where the ligand is located. Could you try run_gist? I did my test with GIST.

Regards,

Anthony

On Tue, Sep 17, 2019 at 5:36 AM Zahratehrani notifications@github.com wrote:

Dear Anthony, Hi.. thanks for your suggestion.... I have changed the extension to .prmtop by making a copy of .top file and test run_hsa and cpptraj in AMBER with files I shared with you. so for run_has, as it was compiled with mini-conda, first I have activated that by: source $HOME/miniconda2/bin/activate then used the following command: run_hsa -i Wat.sdf.prmtop -t sdf-100-frames.nc -l ligand.pdb -s 0 -f 100 -o sdf

Initializing ... Obtaining non-bonded parameters for the system ... Total time running generate_nonbonded_params: 7.56 seconds Done. Assigning hydrogen bond types ... Total time running assign_hb_types: 4.58 seconds Done. Total time running init: 14.67 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: 10.17 seconds Total time running initialize_site_data: 0.00 seconds Total time running initialize_hydration_sites: 10.17 seconds System information: Parameter file:

/auto/plzen1/home/zahratehrani7/STING-MD/GIST-test/2-3-GAMP/test-8/test/Wat.sdf.prmtop

Trajectory: /auto/plzen1/home/zahratehrani7/STING-MD/GIST-test/2-3-GAMP/test-8/test/ sdf-100-frames.nc

Total Atoms: 72376, Waters: 22143, Solute Atoms: 5947

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: 0.33 seconds Generating expanded cluster water files... Segmentation fault (core dumped)

may be I have to recompile it again but it works fine with "testcase" example (prmtop and nc files). in the second test by using cpptraj in AMBER, got all of .dx files but all values are zero! you can find all of inps/outs for both methods in the attachment.

Thanks in advanced Bests Zahra

SSTMap_HSA.zip https://github.com/KurtzmanLab/SSTMap/files/3620440/SSTMap_HSA.zip CPPTRAJ.zip https://github.com/KurtzmanLab/SSTMap/files/3620441/CPPTRAJ.zip

— You are receiving this because you commented. Reply to this email directly, view it on GitHub < https://github.com/KurtzmanLab/SSTMap/issues/100?email_source=notifications&email_token=ACLWJSU442J2UT3WZZSIAEDQKCQKHA5CNFSM4IR7APSKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6355FY#issuecomment-532143767 , or mute the thread < https://github.com/notifications/unsubscribe-auth/ACLWJSTJPKZEZWVZOR2XU53QKCQKHANCNFSM4IR7APSA

.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/KurtzmanLab/SSTMap/issues/100?email_source=notifications&email_token=AGYKFQ6PXBDDGVV2XC2NUF3QKETZDA5CNFSM4IR7APSKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD65S6BI#issuecomment-532360965, or mute the thread https://github.com/notifications/unsubscribe-auth/AGYKFQ3VHIUTW3PMHO5KAGDQKETZDANCNFSM4IR7APSA .

--

---

Tom Kurtzman, Ph.D. Associate Professor Department of Chemistry Lehman College, CUNY 250 Bedford Park Blvd. West Bronx, New York 10468 718-960-8832 http://www.lehman.edu/faculty/tkurtzman/ http://www.lehman.edu/faculty/tkurtzman/index.html

---

[Zahratehrani]

Dear Anthony, Hi.. have tested both GIST (100-selected frames) and HSA (with 2000 frames/20ns).. you can find the results as follow and in the attachment… GIST result is the same I got from CPPTRAJ.. it prints couple of .dx with zero value and HAS is not working (terminated with Segmentation fault (core dumped) error) .. how is about your results? your suggestion will be appreciated… Cheers Zahra GIST: run_gist -i Wat.sdf.prmtop -t sdf-100-frames.nc -l ligand.pdb -g 40 40 40 -s 0 -f 100 -o sdf Initializing ... Obtaining non-bonded parameters for the system ... Total time running generate_nonbonded_params: 6.84 seconds Done. Assigning hydrogen bond types ... Total time running assign_hb_types: 4.53 seconds Done. Initializing ... Total time running init: 14.90 seconds System information: Parameter file: /auto/plzen1/home/zahratehrani7/STING-MD/GIST-test/2-3-GAMP/test-9/gist/Wat.sdf.prmtop Trajectory: /auto/plzen1/home/zahratehrani7/STING-MD/GIST-test/2-3-GAMP/test-9/gist/sdf-100-frames.nc Frames: 100, Total Atoms: 72376, Waters: 22143, Solute Atoms: 5947 Grid information: GIST grid center: -9.005 15.665 -17.441 GIST grid dimensions: 40 40 40 GIST grid spacing: 0.500 A^3 Total referenced orientational entropy of the grid: dTSorient = 0.00000 kcal/mol, Nf=100 Total referenced translational entropy of the grid: dTStrans = 0.00000 kcal/mol, Nf=100 Total 6d if all one vox: 0.00000 kcal/mol Total t if all one vox: 0.00000 kcal/mol Total o if all one vox: -nan kcal/mol Total time running calculate_entropy: 0.00 seconds Total time running calculate_grid_quantities: 2.48 seconds Summary of main calculatio SSTMap_GIST.zip ns: Number of frames processed: 100 Average number of water molecules over the grid: 0 Total Solute-Water Energy over the grid: 0.000000 Total Water-Water Energy over the grid: 0.000000 Writing voxel data ... Total time running write_data: 1.98 seconds Generating dx files ... Total time running generate_dx_files: 1.81 seconds

HSA run_hsa -i Wat.sdf.prmtop -t sdf.nc -l ligand.pdb -s 0 -f 2000 -o sdf Initializing ... Obtaining non-bonded parameters for the system ... Total time running generate_nonbonded_params: 6.72 seconds Done. Assigning hydrogen bond types ... Total time running assign_hb_types: 4.51 seconds Done. Total time running init: 13.33 seconds Reading trajectory for clustering. Performing an initial clustering over 200 frames. Reading trajectory to obtain water molecules for each cluster. Refining initial cluster positions by considering 2000 frames. Final number of clusters: 0 Total time running generate_clusters: 40.70 seconds Total time running initialize_site_data: 0.00 seconds Total time running initialize_hydration_sites: 40.70 seconds System information: Parameter file: /auto/plzen1/home/zahratehrani7/STING-MD/GIST-test/2-3-GAMP/test-9/hsa/Wat.sdf.prmtop Trajectory: /auto/plzen1/home/zahratehrani7/STING-MD/GIST-test/2-3-GAMP/test-9/hsa/sdf.nc Total Atoms: 72376, Waters: 22143, Solute Atoms: 5947 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: 5.43 seconds Generating expanded cluster water files... Segmentation fault (core dumped)

SSTMap_GIST.zip SSTMap_HSA.zip

[acruzpr]

Hi Zahra,Could you please attach your ligand.pdb?Regards,AnthonySent from my Sprint Samsung Galaxy S® 6 edge. -------- Original message --------From: Zahratehrani notifications@github.com Date: 9/18/19 3:18 AM (GMT-05:00) To: KurtzmanLab/SSTMap SSTMap@noreply.github.com Cc: Anthony Cruz anthonycruzpr@gmail.com, Comment comment@noreply.github.com Subject: Re: [KurtzmanLab/SSTMap] getting zero values for all of  gist's term   in output file  (#100) Dear Anthony,

Hi.. have tested both GIST (100-selected frames) and HSA (with 2000 frames/20ns).. you can find the results as follow and in the attachment… GIST result is the same I got from CPPTRAJ.. it prints couple of .dx with zero value and HAS is not working (terminated with Segmentation fault (core dumped) error) .. how is about your results? your suggestion will be appreciated…

Cheers

Zahra

GIST:

run_gist -i Wat.sdf.prmtop -t sdf-100-frames.nc -l ligand.pdb -g 40 40 40 -s 0 -f 100 -o sdf

Initializing ...

Obtaining non-bonded parameters for the system ...

Total time running generate_nonbonded_params: 6.84 seconds

Done.

Assigning hydrogen bond types ...

Total time running assign_hb_types: 4.53 seconds

Done.

Initializing ...

Total time running init: 14.90 seconds

System information:

Parameter file: /auto/plzen1/home/zahratehrani7/STING-MD/GIST-test/2-3-GAMP/test-9/gist/Wat.sdf.prmtop

Trajectory: /auto/plzen1/home/zahratehrani7/STING-MD/GIST-test/2-3-GAMP/test-9/gist/sdf-100-frames.nc

Frames: 100, Total Atoms: 72376, Waters: 22143, Solute Atoms: 5947

Grid information:

GIST grid center: -9.005 15.665 -17.441

GIST grid dimensions: 40 40 40

GIST grid spacing: 0.500 A^3

Total referenced orientational entropy of the grid: dTSorient = 0.00000 kcal/mol, Nf=100

Total referenced translational entropy of the grid: dTStrans = 0.00000 kcal/mol, Nf=100

Total 6d if all one vox: 0.00000 kcal/mol

Total t if all one vox: 0.00000 kcal/mol

Total o if all one vox: -nan kcal/mol

Total time running calculate_entropy: 0.00 seconds

Total time running calculate_grid_quantities: 2.48 seconds

Summary of main calculatio

SSTMap_GIST.zip

ns:

Number of frames processed: 100

Average number of water molecules over the grid: 0

Total Solute-Water Energy over the grid: 0.000000

Total Water-Water Energy over the grid: 0.000000

Writing voxel data ...

Total time running write_data: 1.98 seconds

Generating dx files ...

Total time running generate_dx_files: 1.81 seconds

HSA

run_hsa -i Wat.sdf.prmtop -t sdf.nc -l ligand.pdb -s 0 -f 2000 -o sdf

Initializing ...

Obtaining non-bonded parameters for the system ...

Total time running generate_nonbonded_params: 6.72 seconds

Done.

Assigning hydrogen bond types ...

Total time running assign_hb_types: 4.51 seconds

Done.

Total time running init: 13.33 seconds

Reading trajectory for clustering.

Performing an initial clustering over 200 frames.

Reading trajectory to obtain water molecules for each cluster.

Refining initial cluster positions by considering 2000 frames.

Final number of clusters: 0

Total time running generate_clusters: 40.70 seconds

Total time running initialize_site_data: 0.00 seconds

Total time running initialize_hydration_sites: 40.70 seconds

System information:

Parameter file: /auto/plzen1/home/zahratehrani7/STING-MD/GIST-test/2-3-GAMP/test-9/hsa/Wat.sdf.prmtop

Trajectory: /auto/plzen1/home/zahratehrani7/STING-MD/GIST-test/2-3-GAMP/test-9/hsa/sdf.nc

Total Atoms: 72376, Waters: 22143, Solute Atoms: 5947

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: 5.43 seconds

Generating expanded cluster water files...

Segmentation fault (core dumped)

SSTMap_GIST.zip

SSTMap_HSA.zip

—You are receiving this because you commented.Reply to this email directly, view it on GitHub, or mute the thread.

[

{

"@context": "http://schema.org",

"@type": "EmailMessage",

"potentialAction": {

"@type": "ViewAction",

"target": "https://github.com/KurtzmanLab/SSTMap/issues/100?email_source=notifications\u0026email_token=ACLWJSVSKRGVCCC5HEHUICDQKHI3DA5CNFSM4IR7APSKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD67CFZI#issuecomment-532554469",

"url": "https://github.com/KurtzmanLab/SSTMap/issues/100?email_source=notifications\u0026email_token=ACLWJSVSKRGVCCC5HEHUICDQKHI3DA5CNFSM4IR7APSKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD67CFZI#issuecomment-532554469",

"name": "View Issue"

},

"description": "View this Issue on GitHub",

"publisher": {

"@type": "Organization",

"name": "GitHub",

"url": "https://github.com"

}

}

]

[Zahratehrani]

Hi again... sure.. Cheers

Lig.zip

Zahra

[acruzpr]

Hi Zahra,How you created the ligand.pdb?AnthonySent from my Sprint Samsung Galaxy S® 6 edge. -------- Original message --------From: Zahratehrani notifications@github.com Date: 9/18/19 6:47 AM (GMT-05:00) To: KurtzmanLab/SSTMap SSTMap@noreply.github.com Cc: Anthony Cruz anthonycruzpr@gmail.com, Comment comment@noreply.github.com Subject: Re: [KurtzmanLab/SSTMap] getting zero values for all of  gist's term   in output file  (#100) Hi again... sure.. Cheers Lig.zip Zahra

—You are receiving this because you commented.Reply to this email directly, view it on GitHub, or mute the thread. [ { "@context": "http://schema.org", "@type": "EmailMessage", "potentialAction": { "@type": "ViewAction", "target": "https://github.com/KurtzmanLab/SSTMap/issues/100?email_source=notifications\u0026email_token=ACLWJSVIHUNSZURZKH23YLLQKIBNZA5CNFSM4IR7APSKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD67UWIY#issuecomment-532630307", "url": "https://github.com/KurtzmanLab/SSTMap/issues/100?email_source=notifications\u0026email_token=ACLWJSVIHUNSZURZKH23YLLQKIBNZA5CNFSM4IR7APSKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD67UWIY#issuecomment-532630307", "name": "View Issue" }, "description": "View this Issue on GitHub", "publisher": { "@type": "Organization", "name": "GitHub", "url": "https://github.com" } } ]

[Zahratehrani]

Hi.. its taken out from final pdb file of tleap (solvated protain-lig comaplex) .. opened that pdb with MOE and save the ligand coordinate as .pdb Cheers Zahra

[acruzpr]

Hi Zahra,

The Lig.zip is a link to a file from SSTMap ( https://github.com/KurtzmanLab/SSTMap/files/3625945/Lig.zip) Could you attach yours?

Regards,

Anthony

On Wed, Sep 18, 2019 at 7:09 AM Zahratehrani notifications@github.com wrote:

Hi.. its taken out from final pdb file of tleap (solvated protain-lig comaplex) .. opened that pdb with MOE and save the ligand coordinate as .pdb Cheers Zahra

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/KurtzmanLab/SSTMap/issues/100?email_source=notifications&email_token=ACLWJSU4WSSQGKBR7FZGIJLQKID5XA5CNFSM4IR7APSKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD67WJQI#issuecomment-532636865, or mute the thread https://github.com/notifications/unsubscribe-auth/ACLWJSWM7DKGSIN6DYTLSPDQKID5XANCNFSM4IR7APSA .

[Zahratehrani]

Hi Anthony, I have used the following .pdb for my GIST calc.. Cheers Zahra Lig-zahra.zip

[acruzpr]

Hi Zahra,

Sorry for the misunderstanding with the ligand. I was expecting an actual attachment but I realized that we are doing all this through GitHub.

Ok, the problem is the ligand.pdb. If you visually inspect your ligand you will see that it is outside of the simulation box. In order to avoid this problem, always use a ligand.pdb generated with the restart file from the production stage of your simulation or extracted from any frame of your simulation.

Regards,

Anthony

On Wed, Sep 18, 2019 at 8:30 AM Zahratehrani notifications@github.com wrote:

Hi Anthony, I have used the following .pdb for my GIST calc.. Cheers Zahra Lig-zahra.zip https://github.com/KurtzmanLab/SSTMap/files/3626344/Lig-zahra.zip

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/KurtzmanLab/SSTMap/issues/100?email_source=notifications&email_token=ACLWJSUDCB7BL4N3MUYSYIDQKINO5A5CNFSM4IR7APSKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD674QQI#issuecomment-532662337, or mute the thread https://github.com/notifications/unsubscribe-auth/ACLWJSVV2KCXBIOPFPRMPUDQKINO5ANCNFSM4IR7APSA .

[Zahratehrani]

Dear Anthony, NP..I am sorry for disturbing you couple of times and really appreciate your help.. will take another sample of the ligand as you suggested and test it again...will post the result.. Have a nice aftrenoon Cheers Zahra

[wutobias]

Would it be a good idea to have implemented a sanity check that looks for unusually high distances between the ligand and water molecules and spit out a warning accordingly? That way one could detect ligands outside the simulation box...

Best, Tobias

[tkurtzman]

Yes. That makes sense. Though telling people to visualize the protein-ligand complex should be sufficient (as we did in this case). We should draft up a list of sanity checks.

1) Visually inspect that the protein is restrained and inside the GIST box 2) Visually inspect that the ligand is in the correct region (HSA)

Tom

On Thu, Sep 19, 2019 at 8:43 AM Tobias Hüfner-Wulsdorf < notifications@github.com> wrote:

Would it be a good idea to have implemented a sanity check that looks for unusually high distances between the ligand and water molecules and spit out a warning accordingly? That way one could detect ligands outside the simulation box...

Best, Tobias

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/KurtzmanLab/SSTMap/issues/100?email_source=notifications&email_token=AGYKFQ7UW32TJV7MZYZBMF3QKNXYDA5CNFSM4IR7APSKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD7DKU5Q#issuecomment-533113462, or mute the thread https://github.com/notifications/unsubscribe-auth/AGYKFQ6SXLGBCSQI44ZFPELQKNXYDANCNFSM4IR7APSA .

--

---

Tom Kurtzman, Ph.D. Associate Professor Department of Chemistry Lehman College, CUNY 250 Bedford Park Blvd. West Bronx, New York 10468 718-960-8832 http://www.lehman.edu/faculty/tkurtzman/ http://www.lehman.edu/faculty/tkurtzman/index.html

---

[Zahratehrani]

Hi all, as short update, I have took the ligand from traj as Anthony suggested and both GIST and HSA worked fine (finished with no error ).. I will try to understand the results/output... Thanks for all of your support Cheers Zahra