mglgc commented 1 year ago

Hi, The TTMD running ends with errors immediately after the temperature 300 simulation step. Below I attach the output error lines. Thank you very much in advance for your reply.

———————————————————— RUNNING TTMD ————————————————————

TEMPERATURE 300

——Running 300 simulation ——run_300.dcd found ——Trajectory integrity checked ——Trajectory integrity checked ——sim_300.dat doesn't exists Writing PDBs: 100%|██████████| 500/500 [05:46<00:00, 1.44it/s] Calculating fingerprints: 0%| | 0/500 [00:00<?, ?it/s]Process Process-8: Process Process-5: Traceback (most recent call last): Traceback (most recent call last): File "/mnt/netapp1/Store_CSIC/home/csic/sdb/mgl/conda/envs/ttmd/lib/python3.10/multiprocessing/process.py", line 314, in _bootstrap self.run() File "/mnt/netapp1/Store_CSIC/home/csic/sdb/mgl/conda/envs/ttmd/lib/python3.10/multiprocessing/process.py", line 108, in run self._target(*self._args, self._kwargs) File "/mnt/lustre/scratch/nlsas/home/csic/sdb/mgl/TTMD-main/TTMD.py", line 485, in worker result = func(args) File "/mnt/netapp1/Store_CSIC/home/csic/sdb/mgl/conda/envs/ttmd/lib/python3.10/multiprocessing/process.py", line 314, in _bootstrap self.run() File "/mnt/lustre/scratch/nlsas/home/csic/sdb/mgl/TTMD-main/TTMD.py", line 608, in ifp sim_giovanni=float(sklearn.metrics.pairwise.cosine_similarity(x, y)) File "/mnt/netapp1/Store_CSIC/home/csic/sdb/mgl/conda/envs/ttmd/lib/python3.10/multiprocessing/process.py", line 108, in run self._target(self._args, self._kwargs) File "/mnt/netapp1/Store_CSIC/home/csic/sdb/mgl/conda/envs/ttmd/lib/python3.10/site-packages/sklearn/metrics/pairwise.py", line 1377, in cosine_similarity X, Y = check_pairwise_arrays(X, Y) File "/mnt/lustre/scratch/nlsas/home/csic/sdb/mgl/TTMD-main/TTMD.py", line 485, in worker result = func(args) File "/mnt/netapp1/Store_CSIC/home/csic/sdb/mgl/conda/envs/ttmd/lib/python3.10/site-packages/sklearn/metrics/pairwise.py", line 155, in check_pairwise_arrays X = check_array( File "/mnt/lustre/scratch/nlsas/home/csic/sdb/mgl/TTMD-main/TTMD.py", line 608, in ifp sim_giovanni=float(sklearn.metrics.pairwise.cosine_similarity(x, y)) File "/mnt/netapp1/Store_CSIC/home/csic/sdb/mgl/conda/envs/ttmd/lib/python3.10/site-packages/sklearn/utils/validation.py", line 918, in check_array raise ValueError( File "/mnt/netapp1/Store_CSIC/home/csic/sdb/mgl/conda/envs/ttmd/lib/python3.10/site-packages/sklearn/metrics/pairwise.py", line 1377, in cosine_similarity X, Y = check_pairwise_arrays(X, Y) File "/mnt/netapp1/Store_CSIC/home/csic/sdb/mgl/conda/envs/ttmd/lib/python3.10/site-packages/sklearn/metrics/pairwise.py", line 155, in check_pairwise_arrays X = check_array( ValueError: Found array with 0 feature(s) (shape=(1, 0)) while a minimum of 1 is required by check_pairwise_arrays. File "/mnt/netapp1/Store_CSIC/home/csic/sdb/mgl/conda/envs/ttmd/lib/python3.10/site-packages/sklearn/utils/validation.py", line 918, in check_array raise ValueError( ValueError: Found array with 0 feature(s) (shape=(1, 0)) while a minimum of 1 is required by check_pairwise_arrays. Process Process-6: Traceback (most recent call last): File "/mnt/netapp1/Store_CSIC/home/csic/sdb/mgl/conda/envs/ttmd/lib/python3.10/multiprocessing/process.py", line 314, in _bootstrap self.run() File "/mnt/netapp1/Store_CSIC/home/csic/sdb/mgl/conda/envs/ttmd/lib/python3.10/multiprocessing/process.py", line 108, in run self._target(self._args, self._kwargs) File "/mnt/lustre/scratch/nlsas/home/csic/sdb/mgl/TTMD-main/TTMD.py", line 485, in worker result = func(args) File "/mnt/lustre/scratch/nlsas/home/csic/sdb/mgl/TTMD-main/TTMD.py", line 608, in ifp sim_giovanni=float(sklearn.metrics.pairwise.cosine_similarity(x, y)) File "/mnt/netapp1/Store_CSIC/home/csic/sdb/mgl/conda/envs/ttmd/lib/python3.10/site-packages/sklearn/metrics/pairwise.py", line 1377, in cosine_similarity X, Y = check_pairwise_arrays(X, Y) File "/mnt/netapp1/Store_CSIC/home/csic/sdb/mgl/conda/envs/ttmd/lib/python3.10/site-packages/sklearn/metrics/pairwise.py", line 155, in check_pairwise_arrays X = check_array( File "/mnt/netapp1/Store_CSIC/home/csic/sdb/mgl/conda/envs/ttmd/lib/python3.10/site-packages/sklearn/utils/validation.py", line 918, in check_array raise ValueError( ValueError: Found array with 0 feature(s) (shape=(1, 0)) while a minimum of 1 is required by check_pairwise_arrays. Process Process-7: Traceback (most recent call last): File "/mnt/netapp1/Store_CSIC/home/csic/sdb/mgl/conda/envs/ttmd/lib/python3.10/multiprocessing/process.py", line 314, in _bootstrap self.run() File "/mnt/netapp1/Store_CSIC/home/csic/sdb/mgl/conda/envs/ttmd/lib/python3.10/multiprocessing/process.py", line 108, in run self._target(self._args, self._kwargs) File "/mnt/lustre/scratch/nlsas/home/csic/sdb/mgl/TTMD-main/TTMD.py", line 485, in worker result = func(*args) File "/mnt/lustre/scratch/nlsas/home/csic/sdb/mgl/TTMD-main/TTMD.py", line 608, in ifp sim_giovanni=float(sklearn.metrics.pairwise.cosine_similarity(x, y)) File "/mnt/netapp1/Store_CSIC/home/csic/sdb/mgl/conda/envs/ttmd/lib/python3.10/site-packages/sklearn/metrics/pairwise.py", line 1377, in cosine_similarity X, Y = check_pairwise_arrays(X, Y) File "/mnt/netapp1/Store_CSIC/home/csic/sdb/mgl/conda/envs/ttmd/lib/python3.10/site-packages/sklearn/metrics/pairwise.py", line 155, in check_pairwise_arrays X = check_array( File "/mnt/netapp1/Store_CSIC/home/csic/sdb/mgl/conda/envs/ttmd/lib/python3.10/site-packages/sklearn/utils/validation.py", line 918, in check_array raise ValueError( ValueError: Found array with 0 feature(s) (shape=(1, 0)) while a minimum of 1 is required by check_pairwise_arrays.

molecularmodelingsection commented 1 year ago

Hi, it seems that there might be a problem with the calculation of the interaction fingerprint for your system. Unfortunately, there are several things that could cause this issue. Could you please provide us with the input files that you are using so that we can play around a little bit and try to come back at you with a solution? MP

mglgc commented 1 year ago

Hi,Attached you'll find the protein and ligand files. Thank you very much for your help and replies.Sincerely, Mario.

En lunes, 5 de junio de 2023 6:05:10 CEST, Molecular Modeling Section ***@***.***> escribió:

Hi, it seems that there might be a problem with the calculation of the interaction fingerprint for your system. Unfortunately, there are several things that could cause this issue. Could you please provide us with the input files that you are using so that we can play around a little bit and try to come back at you with a solution? MP

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>

molecularmodelingsection commented 1 year ago

Hi, Sorry, but we can't find your files. Could you please attach them again or send them to mms.dsfarm.unipd@gmail.com? Thanks a lot MP

mglgc commented 1 year ago

Hi,I have just sent the files to @.*** Thank you very much for your replies.Regards.

En martes, 6 de junio de 2023 18:35:35 CEST, Molecular Modeling Section ***@***.***> escribió:

Hi, Sorry, but we can't find your files. Could you please attach them again or send them to @.***? Thanks a lot MP

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>

molecularmodelingsection commented 1 year ago

Hi, sorry for the late response but during the last month the two maintainers had to deal with a surgical operation and with a relocation, respectively. We hope that you will be able to understand. I did some testing on the files that you provided us and I found nothing wrong. Indeed, the system works smoothly and I am able to correctly run a TTMD simulation in all its stages (including the plotting and MS coefficient calculation). The only thing that I found strange was that the protein had two naming issues (HIS 272 and 465 were not named according to the AMBER naming scheme and were renamed as HIP) but, after solving this minor inconvenience in the system preparation stage, the protocol went on without any trouble until the very end. I don't even know if the protein file that you provided is the same one that you used when you obtained that error, because if that was the case you should not have been able to proceed past the system preparation step without addressing this naming issue. Maybe you inadvertently sent us the wrong file, we do not know, but with the files you provided us everything seems to work just fine. Based on our experience, when the system crashes like this it is usually because the reference fingerprint is null, indicating that there are no computed interactions between the receptor and the ligand, which makes the script crash at a later stage in the fingerprint comparison stage. It is something that we are working on at the moment and that will be fixed in the next release of the software (hopefully it will come out in the next months), but it is just related to the way the script handles the null fingerprint, it will not solve the lack of interactions found in your system. That can depend on two factors: wrong geometry or wrong atom typing. Considering that both those elements seem to be okay in the files that you provided us and that the simulation seems to run just fine, I do not know what to say, other than checking that you provided us the right files (especially the protein), or that you try running the simulation once again. I will send you via email the exact same files (plus an updated conda env that I needed to use cause of the acemd version which is not compatible with the GPU I am currently running), so that you can try and see if the problem still exists or if, somehow, it is solved. MP

molecularmodelingsection commented 1 year ago

Hi, here are the files that I used for the test run that worked. Let us know if you managed to solve the issue. Kind regards, MP

Il giorno mer 7 giu 2023 alle ore 04:55 mglgc @.***> ha scritto:

Hi,I have just sent the files to @.*** Thank you very much for your replies.Regards.

En martes, 6 de junio de 2023 18:35:35 CEST, Molecular Modeling Section @.***> escribió:

Hi, Sorry, but we can't find your files. Could you please attach them again or send them to @.***? Thanks a lot MP

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>

— Reply to this email directly, view it on GitHub https://github.com/molecularmodelingsection/TTMD/issues/9#issuecomment-1580234737, or unsubscribe https://github.com/notifications/unsubscribe-auth/A2KJ4CUHFDCGSHSGAETR4HTXKA6XFANCNFSM6AAAAAAYVYJQUM . You are receiving this because you commented.Message ID: @.***>

This file may be used to create an environment using:

$ conda create --name --file

platform: linux-64

mglgc commented 1 year ago

Dear Stefano, I really want to thank your kind and quite useful reply. I'm pretty sure about both of files I sent you, anyway I'll check them and run them again, so I close this issue for the moment. Thank you very much once again for all your time and help. Best regards.

Hi, sorry for the late response but during the last month the two maintainers had to deal with a surgical operation and with a relocation, respectively. We hope that you will be able to understand. I did some testing on the files that you provided us and I found nothing wrong. Indeed, the system works smoothly and I am able to correctly run a TTMD simulation in all its stages (including the plotting and MS coefficient calculation). The only thing that I found strange was that the protein had two naming issues (HIS 272 and 465 were not named according to the AMBER naming scheme and were renamed as HIP) but, after solving this minor inconvenience in the system preparation stage, the protocol went on without any trouble until the very end. I don't even know if the protein file that you provided is the same one that you used when you obtained that error, because if that was the case you should not have been able to proceed past the system preparation step without addressing this naming issue. Maybe you inadvertently sent us the wrong file, we do not know, but with the files you provided us everything seems to work just fine. Based on our experience, when the system crashes like this it is usually because the reference fingerprint is null, indicating that there are no computed interactions between the receptor and the ligand, which makes the script crash at a later stage in the fingerprint comparison stage. It is something that we are working on at the moment and that will be fixed in the next release of the software (hopefully it will come out in the next months), but it is just related to the way the script handles the null fingerprint, it will not solve the lack of interactions found in your system. That can depend on two factors: wrong geometry or wrong atom typing. Considering that both those elements seem to be okay in the files that you provided us and that the simulation seems to run just fine, I do not know what to say, other than checking that you provided us the right files (especially the protein), or that you try running the simulation once again. I will send you via email the exact same files (plus an updated conda env that I needed to use cause of the acemd version which is not compatible with the GPU I am currently running), so that you can try and see if the problem still exists or if, somehow, it is solved. MP

molecularmodelingsection / TTMD

Error calculating fingerprints #9

Hi, The TTMD running ends with errors immediately after the temperature 300 simulation step. Below I attach the output error lines. Thank you very much in advance for your reply.

This file may be used to create an environment using:

$ conda create --name --file

platform: linux-64