Unable to install in LinuxMint #121
Comments
|
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/. |
|
yes also installed kiwisolver>=1.0.1. And it installed. Thanks. The issue solved. Thanks a lot |
|
but during test encountered by following error (sstmap) debanjan@debanjan:~/Downloads/sstmap_test_suite$ make test_quick Grid information: Total referenced orientational entropy of the grid: dTSorient = -226.37442 kcal/mol, Nf=100 Arrays are not almost equal to 3 decimals Mismatch: 4.65% Arrays are not almost equal to 3 decimals Mismatch: 14.1% Arrays are not almost equal to 3 decimals Mismatch: 1.17% Reading trajectory for clustering. |
|
Error in make test_water (sstmap) debanjan@debanjan:~/Downloads/sstmap_test_suite$ make test_water Grid information: Total referenced orientational entropy of the grid: dTSorient = -0.12832 kcal/mol, Nf=100 Grid information: Total referenced orientational entropy of the grid: dTSorient = 1.20519 kcal/mol, Nf=100 |
|
Hi,
Sorry for the delay, but I was working.
There are 2 things that you can try.
The first option is to create a new Python environment with python=3.6 and
numpy=1.17. Using GCC and GXX v7 and gsl try to install SSTMap again.
For the second option, clone the SSTMap repository and check out the
*all_conda* branch. Then use sstmap_conda_env.yml to create the conda
environment and install SSTMap. These are the changes I recently tested to
install SSTMap in an HPC cluster without requiring the installation of
additional packages from the system. This should work in any Linux
distribution because it uses only resources provided by conda (gcc, gxx,
and gsl).
Could you try the test suite again after any of the options above?
Let me know if this work for you.
Regards,
Anthony
…On Mon, Jul 31, 2023 at 3:41 PM debanjansen48 ***@***.***> wrote:
*Error in make test_water*
(sstmap) ***@***.***:~/Downloads/sstmap_test_suite$ *make
test_water*
cd tests/; python test_water_models.py
Testing: tip3p
Initializing ...
Obtaining non-bonded parameters for the system ...
Total time running generate_nonbonded_params: 0.24 seconds
Done.
Assigning hydrogen bond types ...
Total time running assign_hb_types: 0.01 seconds
Done.
Initializing ...
Total time running *init*: 0.38 seconds
System information:
Parameter file:
/home/debanjan/Downloads/sstmap_test_suite/water_models/tip3p/tip3p.prmtop
Trajectory: /home/debanjan/Downloads/sstmap_test_suite/water_models/tip3p/md100ps.nc
Frames: 100, Total Atoms: 7743, Waters: 2581, Solute Atoms: 0
Grid information:
GIST grid center: 22.506 22.156 21.516
GIST grid dimensions: 20 20 20
GIST grid spacing: 0.500 A^3
Total referenced orientational entropy of the grid: dTSorient = -0.12832
kcal/mol, Nf=100
Total referenced translational entropy of the grid: dTStrans = -0.15166
kcal/mol, Nf=100
Total 6d if all one vox: -0.29620 kcal/mol
Total t if all one vox: -0.00646 kcal/mol
Total o if all one vox: 0.22335 kcal/mol
Total time running calculate_entropy: 0.00 seconds
Total time running calculate_grid_quantities: 3.24 seconds
Writing voxel data ...
Total time running write_data: 0.14 seconds
Summary of main calculations:
Number of frames processed: 100
Average number of water molecules over the grid: 10
Total Solute-Water Energy over the grid: 0.000000
Total Water-Water Energy over the grid: -105.056113
Generating dx files ...
Total time running generate_dx_files: 0.07 seconds
Testing: tip4p
Initializing ...
Obtaining non-bonded parameters for the system ...
Total time running generate_nonbonded_params: 2.28 seconds
Done.
Assigning hydrogen bond types ...
Total time running assign_hb_types: 0.06 seconds
Done.
Initializing ...
Total time running *init*: 3.19 seconds
System information:
Parameter file:
/home/debanjan/Downloads/sstmap_test_suite/water_models/tip4p/tip4p.prmtop
Trajectory: /home/debanjan/Downloads/sstmap_test_suite/water_models/tip4p/md100ps.nc
Frames: 100, Total Atoms: 73244, Waters: 18311, Solute Atoms: 0
Grid information:
GIST grid center: 40.401 40.848 41.257
GIST grid dimensions: 20 20 20
GIST grid spacing: 0.500 A^3
Total referenced orientational entropy of the grid: dTSorient = 1.20519
kcal/mol, Nf=100
Total referenced translational entropy of the grid: dTStrans = -0.24382
kcal/mol, Nf=100
Total 6d if all one vox: -0.13013 kcal/mol
Total t if all one vox: -0.01002 kcal/mol
Total o if all one vox: 0.26619 kcal/mol
Total time running calculate_entropy: 0.02 seconds
Total time running calculate_grid_quantities: 49.78 seconds
Writing voxel data ...
Total time running write_data: 0.80 seconds
Summary of main calculations:
Number of frames processed: 100
Average number of water molecules over the grid: 11
Total Solute-Water Energy over the grid: 0.000000
Total Water-Water Energy over the grid: -109.705456
Generating dx files ...
Total time running generate_dx_files: 0.39 seconds
Testing: tip4pew
Initializing ...
Obtaining non-bonded parameters for the system ...
Segmentation fault (core dumped)
make: *** [Makefile:11: test_water] Error 139
—
Reply to this email directly, view it on GitHub
<#121 (comment)>,
or unsubscribe
<https://github.com/notifications/unsubscribe-auth/ACLWJSTTWNH7HEBLLO5TSADXTAC6DANCNFSM6AAAAAA26FLYFA>
.
You are receiving this because you are subscribed to this thread.Message
ID: ***@***.***>
|
|
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 |
|
sir, from where i will get the sstmap_conda_env.yml file? Its not in the git reposetory. Thanks |
|
You need to check out the *all_conda *branch that I created yesterday.
*git clone https://github.com/KurtzmanLab/SSTMap.git
<https://github.com/KurtzmanLab/SSTMap.git>*
then from within the SSTMap repository
*git checkout all_conda*
Then you will see the file and will have all the changes to use that
environment.
…On Tue, Aug 1, 2023 at 1:35 AM debanjansen48 ***@***.***> wrote:
sir, from where i will get the sstmap_conda_env.yml file? Its not in the
git reposetory. Thanks
—
Reply to this email directly, view it on GitHub
<#121 (comment)>,
or unsubscribe
<https://github.com/notifications/unsubscribe-auth/ACLWJSV6PVQPVXVMJDJBQY3XTCIT5ANCNFSM6AAAAAA26FLYFA>
.
You are receiving this because you commented.Message ID:
***@***.***>
|
|
(base) debanjan@debanjan:~$ conda create -n sstmap_py36 python=3.6 Package Planenvironment 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 Proceed ([y]/n)? y Downloading and Extracting Packages Preparing transaction: done To activate this environment, use$ conda activate sstmap_py36To deactivate an active environment, use$ conda deactivate(base) debanjan@debanjan: |
|
You need to be inside the SSTMap directory to check out the branch. |
Arrays are not almost equal to 3 decimals Mismatch: 1.17% 2. make test_hsa OK
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. |
|
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 |
|
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 Writing PDB file containing all HSA region water molecules for entropy calculations. |
|
In order to detect the issue as the test suit provided with the software was considered. Reading trajectory for clustering. Reading trajectory for clustering. Reading trajectory for clustering. Reading trajectory for clustering. |
|
Few questions:
1) How long is your simulation?
2) Which water model are you using?
3) What force field are you using?
4) Please, describe your system. What is inside your simulation box?
(Nothing specific)
5) Did you use restraints in the protein?
6) Did you visually inspect your systems? The ligand.pdb is in the binding
site?
7) What's your background? Chemistry/Biology/Physics? Are you a student?
BS/MS/PhD?
8) Have you looked at the posts in sstmap.org
9) Have you read the paper?
“Solvation Structure and Thermodynamic Mapping (SSTMap): An Open-Source,
Flexible Package for the Analysis of Water in Molecular Dynamics
Trajectories” published in the Journal of Chemical Theory and
Computation: DOI:
10.1021/acs.jctc.7b00592 <http://pubs.acs.org/doi/10.1021/acs.jctc.7b00592>.
…On Wed, Aug 2, 2023 at 12:25 PM debanjansen48 ***@***.***> wrote:
In order to detect the issue as the test suit provided with the software
was considered.
inside the gromacs directory i placed my md files and rename accordingly.
after execution again getting error. Which means there was some issue with
my setup.
(sstmap) ***@***.***:~/Downloads/sstmap_test_suite$ make test_hsa
cd tests/; python test_platforms_hsa.py
Testing: amber
Initializing ...
Obtaining non-bonded parameters for the system ...
Total time running generate_nonbonded_params: 0.11 seconds
Done.
Assigning hydrogen bond types ...
Total time running assign_hb_types: 0.00 seconds
Done.
Total time running *init*: 0.15 seconds
System information:
Parameter file:
/home/debanjan/Downloads/sstmap_test_suite/platforms/amber/testcase.prmtop
Trajectory: /home/debanjan/Downloads/sstmap_test_suite/platforms/amber/md100ps.nc
Total Atoms: 3026, Waters: 1001, Solute Atoms: 23
Reading trajectory for clustering.
Performing an initial clustering over 10 frames.
Reading trajectory to obtain water molecules for each cluster.
Refining initial cluster positions by considering 100 frames.
Final number of clusters: 25
Total time running generate_clusters: 0.13 seconds
Total time running initialize_site_data: 0.00 seconds
Total time running initialize_hydration_sites: 0.13 seconds
Writing PDB file containing all HSA region water molecules for entropy
calculations.
Done.
Writing PDB files for all water molecules in each hydration site.
Done.
Total time running generate_data_for_entropycalcs: 0.06 seconds
Generating expanded cluster water files...
Running entropy calculation from extension module.
Total time running run_entropy_scripts: 0.03 seconds
Total time running normalize_site_quantities: 0.00 seconds
Total time running calculate_site_quantities: 2.02 seconds
Total time running write_calculation_summary: 0.00 seconds
Total time running write_data: 0.02 seconds
Testing: charmm
Initializing ...
Obtaining non-bonded parameters for the system ...
/home/debanjan/miniconda3/envs/sstmap/lib/python3.6/site-packages/parmed/charmm/parameters.py:867:
UserWarning: WARNING: Ignoring "DELETE ACCE NE2" because entity type ACCE
not used.
'used.' % (line.strip(), entity_type))
/home/debanjan/miniconda3/envs/sstmap/lib/python3.6/site-packages/parmed/charmm/parameters.py:747:
ParameterWarning: Atom type CC1A not present in AtomType list
warnings.warn('Atom type %s not present in AtomType list' % key,
ParameterWarning)
Total time running generate_nonbonded_params: 0.33 seconds
Done.
Assigning hydrogen bond types ...
Total time running assign_hb_types: 0.13 seconds
Done.
Total time running *init*: 0.75 seconds
System information:
Parameter file:
/home/debanjan/Downloads/sstmap_test_suite/platforms/charmm/testcase.psf
Trajectory: /home/debanjan/Downloads/sstmap_test_suite/platforms/charmm/md100ps.dcd
Total Atoms: 7051, Waters: 1940, Solute Atoms: 1231
Reading trajectory for clustering.
Performing an initial clustering over 11 frames.
Reading trajectory to obtain water molecules for each cluster.
Refining initial cluster positions by considering 100 frames.
Final number of clusters: 5
Total time running generate_clusters: 0.34 seconds
Total time running initialize_site_data: 0.00 seconds
Total time running initialize_hydration_sites: 0.34 seconds
Writing PDB file containing all HSA region water molecules for entropy
calculations.
Done.
Writing PDB files for all water molecules in each hydration site.
Done.
Total time running generate_data_for_entropycalcs: 0.01 seconds
Generating expanded cluster water files...
Running entropy calculation from extension module.
Total time running run_entropy_scripts: 0.01 seconds
Total time running normalize_site_quantities: 0.00 seconds
Total time running calculate_site_quantities: 1.58 seconds
Total time running write_calculation_summary: 0.00 seconds
Total time running write_data: 0.00 seconds
Testing: desmond
Initializing ...
Obtaining non-bonded parameters for the system ...
Total time running generate_nonbonded_params: 0.01 seconds
Done.
Assigning hydrogen bond types ...
Total time running assign_hb_types: 0.00 seconds
Done.
Total time running *init*: 0.07 seconds
System information:
Parameter file:
/home/debanjan/Downloads/sstmap_test_suite/platforms/desmond/testcase.pdb
Trajectory: /home/debanjan/Downloads/sstmap_test_suite/platforms/desmond/md100ps.nc
Total Atoms: 3026, Waters: 1001, Solute Atoms: 23
Reading trajectory for clustering.
Performing an initial clustering over 10 frames.
Reading trajectory to obtain water molecules for each cluster.
Refining initial cluster positions by considering 100 frames.
Final number of clusters: 25
Total time running generate_clusters: 0.19 seconds
Total time running initialize_site_data: 0.00 seconds
Total time running initialize_hydration_sites: 0.20 seconds
Writing PDB file containing all HSA region water molecules for entropy
calculations.
Done.
Writing PDB files for all water molecules in each hydration site.
Done.
Total time running generate_data_for_entropycalcs: 0.06 seconds
Generating expanded cluster water files...
Running entropy calculation from extension module.
Total time running run_entropy_scripts: 0.03 seconds
Total time running normalize_site_quantities: 0.00 seconds
Total time running calculate_site_quantities: 2.08 seconds
Total time running write_calculation_summary: 0.00 seconds
Total time running write_data: 0.02 seconds
Testing: gromacs
Initializing ...
Obtaining non-bonded parameters for the system ...
Total time running generate_nonbonded_params: 4.30 seconds
Done.
Assigning hydrogen bond types ...
Total time running assign_hb_types: 0.64 seconds
Done.
Total time running *init*: 5.26 seconds
System information:
Parameter file:
/home/debanjan/Downloads/sstmap_test_suite/platforms/gromacs/testcase.gro
Trajectory: /home/debanjan/Downloads/sstmap_test_suite/platforms/gromacs/md100ps.xtc
Total Atoms: 33941, Waters: 10032, Solute Atoms: 3845
Reading trajectory for clustering.
Performing an initial clustering over 10 frames.
Reading trajectory to obtain water molecules for each cluster.
Refining initial cluster positions by considering 100 frames.
Final number of clusters: 0
Total time running generate_clusters: 1.45 seconds
Total time running initialize_site_data: 0.00 seconds
Total time running initialize_hydration_sites: 1.45 seconds
Writing PDB file containing all HSA region water molecules for entropy
calculations.
Done.
Writing PDB files for all water molecules in each hydration site.
Done.
Total time running generate_data_for_entropycalcs: 0.09 seconds
Generating expanded cluster water files...
Segmentation fault (core dumped)
make: *** [Makefile:5: test_hsa] Error 139
if u guide i will be grateful.
—
Reply to this email directly, view it on GitHub
<#121 (comment)>,
or unsubscribe
<https://github.com/notifications/unsubscribe-auth/ACLWJSQQGDOMNUIWDO45FELXTJ5P7ANCNFSM6AAAAAA26FLYFA>
.
You are receiving this because you commented.Message ID:
***@***.***>
|
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. |
|
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
<#121 (comment)>,
or unsubscribe
<https://github.com/notifications/unsubscribe-auth/ACLWJSVVU5GMA37PEI2MJF3XTM4CFANCNFSM6AAAAAA26FLYFA>
.
You are receiving this because you commented.Message ID:
***@***.***>
|
|
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
> <
#121 (comment)>,
> or unsubscribe
> <
https://github.com/notifications/unsubscribe-auth/ACLWJSVVU5GMA37PEI2MJF3XTM4CFANCNFSM6AAAAAA26FLYFA>
> .
> You are receiving this because you commented.Message ID:
> ***@***.***>
>
—
Reply to this email directly, view it on GitHub
<#121 (comment)>,
or unsubscribe
<https://github.com/notifications/unsubscribe-auth/AOJ7Q4VDGIGTXHIRJYFRD63XTRDOPANCNFSM6AAAAAA26FLYFA>
.
You are receiving this because you authored the thread.Message ID:
***@***.***>
|
|
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
|
|
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
1. The answer to this question is in the Olson paper that I
recommended.
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.
1. The answer to this is in the GIST tutorial and the Olson paper.
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
1. 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
—
Reply to this email directly, view it on GitHub
<#121 (comment)>,
or unsubscribe
<https://github.com/notifications/unsubscribe-auth/ACLWJSXNG2JKF4CIHUF35ITXTTQQBANCNFSM6AAAAAA26FLYFA>
.
You are receiving this because you commented.Message ID:
***@***.***>
|
|
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.
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
1. The answer to this question is in the Olson paper that I
recommended.
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.
1. The answer to this is in the GIST tutorial and the Olson paper.
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
1. 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
>
> —
> Reply to this email directly, view it on GitHub
> <
#121 (comment)>,
> or unsubscribe
> <
https://github.com/notifications/unsubscribe-auth/ACLWJSXNG2JKF4CIHUF35ITXTTQQBANCNFSM6AAAAAA26FLYFA>
> .
> You are receiving this because you commented.Message ID:
> ***@***.***>
>
—
Reply to this email directly, view it on GitHub
<#121 (comment)>,
or unsubscribe
<https://github.com/notifications/unsubscribe-auth/AOJ7Q4V7DYDO4HVGC7N3RATXTT4ULANCNFSM6AAAAAA26FLYFA>
.
You are receiving this because you authored the thread.Message ID:
***@***.***>
|
|
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?] |
|
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.
—
Reply to this email directly, view it on GitHub
<#121 (comment)>,
or unsubscribe
<https://github.com/notifications/unsubscribe-auth/ACLWJSVVCFDN3L23UW5GG5DXTZE55ANCNFSM6AAAAAA26FLYFA>
.
You are receiving this because you commented.Message ID:
***@***.***>
|
|
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.
>
> —
> Reply to this email directly, view it on GitHub
> <
#121 (comment)>,
> or unsubscribe
> <
https://github.com/notifications/unsubscribe-auth/ACLWJSVVCFDN3L23UW5GG5DXTZE55ANCNFSM6AAAAAA26FLYFA>
> .
> You are receiving this because you commented.Message ID:
> ***@***.***>
>
—
Reply to this email directly, view it on GitHub
<#121 (comment)>,
or unsubscribe
<https://github.com/notifications/unsubscribe-auth/AOJ7Q4VMT6VYFU4JIOYLZ6TXTZMG3ANCNFSM6AAAAAA26FLYFA>
.
You are receiving this because you authored the thread.Message ID:
***@***.***>
|
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
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.
The text was updated successfully, but these errors were encountered: