The topology and DCD trajectory files don't have the same number of atoms

[saranthee]

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

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]

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: ***@***.***>

[saranthee]

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: > ***@***.***> >

[kulibour]

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)")