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molecularmodelingsection / TTMD

Python code to run Thermal Titration Molecular Dynamics (TTMD) simulations
MIT License
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The topology and DCD trajectory files don't have the same number of atoms #12

Open saranthee opened 7 months ago

saranthee commented 7 months ago

Dear Sir

I am trying TTMD calculation with default config_rt.dat files provided by you. I am getting following errors, please help me to solve this problem

Traceback (most recent call last): File "/mnt/d/TTMD-2.0/package/ttmd.py", line 150, in RUN_class.run(VARS) File "/mnt/d/TTMD-2.0/package/ttmd.py", line 55, in run self.serial(vars) File "/mnt/d/TTMD-2.0/package/ttmd.py", line 65, in serial replica_run(i, self.device, vars) File "/mnt/d/TTMD-2.0/package/ttmd.py", line 114, in replica_run REPLICA_class.simulation() File "/mnt/d/TTMD-2.0/package/replica.py", line 52, in simulation simulation.run() File "/mnt/d/TTMD-2.0/package/simulation/run.py", line 38, in run avg = self.score_simulation(trj, i, set) File "/mnt/d/TTMD-2.0/package/simulation/run.py", line 174, in score_simulation outscore = self.score(self.complprmtop, wrap_trj, temp) File "/mnt/d/TTMD-2.0/package/scoring_function/rt.py", line 52, in score u = mda.Universe(topology, trajectory) File "/home/drsaravanan/miniconda3/envs/ttmd2/lib/python3.10/site-packages/MDAnalysis/core/universe.py", line 365, in init self.load_new(coordinates, format=format, in_memory=in_memory, File "/home/drsaravanan/miniconda3/envs/ttmd2/lib/python3.10/site-packages/MDAnalysis/core/universe.py", line 569, in load_new raise ValueError("The topology and {form} trajectory files don't" ValueError: The topology and DCD trajectory files don't have the same number of atoms! Topology number of atoms 6116 Trajectory: run_300.dcd Number of atoms 76588 error.txt

Please check error.txt file

ghost commented 7 months ago

Dear Saranthee, this issue is generated by a bug in the code. It should be easily overcome by setting "dryer = yes" in the config file. We are grateful for your patience and perseverance in using ttmd and we apologize for the inconvenience. Kind regards, Silvia

saranthee commented 7 months ago

Dear Molecularmodelingsection/Ttmd,

The command "dryer=yes" is already available in the config file. In the RUN_1/MD/ path, I got run_300, dry_300, and swag_300 files already. It is taking automatically wrong prmtop file. It should take solv. prmtop and run_300.dcd or dry_complex.prmtop with dry_300.dcd.

I have tried for three different complexes it is not working

also, I removed ttmd and reinstall ttmd it is not working

I kindly request you please help me to solve this problem If you ready to check the files i will send you or i will give access to my computer to check. Please help to solve this

On Tue, Apr 9, 2024 at 3:01 PM silviett @.***> wrote:

Dear Saranthee, this issue is generated by a bug in the code. It should be easily overcome by setting "dryer = yes" in the config file. We are grateful for your patience and perseverance in using ttmd and we apologize for the inconvenience. Kind regards, Silvia

— Reply to this email directly, view it on GitHub https://github.com/molecularmodelingsection/TTMD/issues/12#issuecomment-2045129851, or unsubscribe https://github.com/notifications/unsubscribe-auth/BFTFUOY4YVYMRC4W4OWJFULY4PRCFAVCNFSM6AAAAABFWZY2WWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANBVGEZDSOBVGE . You are receiving this because you authored the thread.Message ID: @.***>

saranthee commented 5 months ago

Dear TTMD group,

I am eagerly anticipating your response. Kindly inform me if you are prepared to engage in collaborative research work. I possess a collection of complexes and require TTMD results. Please inform me at your earliest convenience.

On Tue, Apr 9, 2024 at 3:39 PM Saravanan Kandasamy @.***> wrote:

Dear Molecularmodelingsection/Ttmd,

The command "dryer=yes" is already available in the config file. In the RUN_1/MD/ path, I got run_300, dry_300, and swag_300 files already. It is taking automatically wrong prmtop file. It should take solv. prmtop and run_300.dcd or dry_complex.prmtop with dry_300.dcd.

I have tried for three different complexes it is not working

also, I removed ttmd and reinstall ttmd it is not working

I kindly request you please help me to solve this problem If you ready to check the files i will send you or i will give access to my computer to check. Please help to solve this

On Tue, Apr 9, 2024 at 3:01 PM silviett @.***> wrote:

Dear Saranthee, this issue is generated by a bug in the code. It should be easily overcome by setting "dryer = yes" in the config file. We are grateful for your patience and perseverance in using ttmd and we apologize for the inconvenience. Kind regards, Silvia

— Reply to this email directly, view it on GitHub https://github.com/molecularmodelingsection/TTMD/issues/12#issuecomment-2045129851, or unsubscribe https://github.com/notifications/unsubscribe-auth/BFTFUOY4YVYMRC4W4OWJFULY4PRCFAVCNFSM6AAAAABFWZY2WWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANBVGEZDSOBVGE . You are receiving this because you authored the thread.Message ID: @.***>

kulibour commented 3 months ago

Dear TTMD group, I am eagerly anticipating your response. Kindly inform me if you are prepared to engage in collaborative research work. I possess a collection of complexes and require TTMD results. Please inform me at your earliest convenience. On Tue, Apr 9, 2024 at 3:39 PM Saravanan Kandasamy @.> wrote: … Dear Molecularmodelingsection/Ttmd, The command "dryer=yes" is already available in the config file. In the RUN_1/MD/ path, I got run_300, dry_300, and swag_300 files already. It is taking automatically wrong prmtop file. It should take solv. prmtop and run_300.dcd or dry_complex.prmtop with dry_300.dcd. I have tried for three different complexes it is not working also, I removed ttmd and reinstall ttmd it is not working I kindly request you please help me to solve this problem If you ready to check the files i will send you or i will give access to my computer to check. Please help to solve this On Tue, Apr 9, 2024 at 3:01 PM silviett @.> wrote: > Dear Saranthee, > this issue is generated by a bug in the code. > It should be easily overcome by setting "dryer = yes" in the config file. > We are grateful for your patience and perseverance in using ttmd and we > apologize for the inconvenience. > Kind regards, > Silvia > > — > Reply to this email directly, view it on GitHub > <#12 (comment)>, > or unsubscribe > https://github.com/notifications/unsubscribe-auth/BFTFUOY4YVYMRC4W4OWJFULY4PRCFAVCNFSM6AAAAABFWZY2WWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANBVGEZDSOBVGE > . > You are receiving this because you authored the thread.Message ID: > @.***> >

  1. cd TTMD/package/simulation/
  2. vi run.py and locate line 38
  3. Replace trj with traj. (I think it should look like "avg = self.score_simulation(traj, i, set)")