Discussion around computational chemistry and cheminformatics tools for the Galaxy platform
I am getting this error.
You can also try nglviewer which doesn't require a download: http://nglviewer.org/ngl/
@anamika-8 Hi , I agree with @simonbray and also recommend nglviewer. If you are still wanting to use VMD on mac, see this article https://support.apple.com/en-us/HT202491 and read the section "How to open an app that hasn’t been notarized or is from an unidentified developer"
it seems to be a problem with the complex prmtop file generated by parmed, I am using the strip mask
:NA,CL,SOL
Maybe you have a suggestion?
Hi @simonbray:matrix.org I made some progress in the draft PR galaxycomputationalchemistry/galaxy-tools-compchem#75 which is now out of date and needs work. Issues could be that there is zero period dihedral in the prmtop (I recall added by leap or gmx somehow but under correction). The other option is to change the strip mask for example if the solution is really named WAT then update as appropriate.
Thanks @chrisbarnettster - I'll check out your branch locally and try rerunning the tool
So after using the 'remove dihedral' option from your branch the 'invalid periodicity' message has gone. But I still get this traceback:
File "/home/simon/miniconda3/envs/mulled-v1-f92559d7ddcee3e1dff9f320232c68156b715c284f93ddfb999897c9d92d55ed/bin/MMPBSA.py", line 100, in <module>
app.run_mmpbsa()
File "/home/simon/miniconda3/envs/mulled-v1-f92559d7ddcee3e1dff9f320232c68156b715c284f93ddfb999897c9d92d55ed/lib/python3.9/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/home/simon/miniconda3/envs/mulled-v1-f92559d7ddcee3e1dff9f320232c68156b715c284f93ddfb999897c9d92d55ed/lib/python3.9/site-packages/MMPBSA_mods/calculation.py", line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/home/simon/miniconda3/envs/mulled-v1-f92559d7ddcee3e1dff9f320232c68156b715c284f93ddfb999897c9d92d55ed/lib/python3.9/site-packages/MMPBSA_mods/calculation.py", line 156, in run
raise CalcError('%s failed with prmtop %s!' % (self.program,
CalcError: /home/simon/miniconda3/envs/mulled-v1-f92559d7ddcee3e1dff9f320232c68156b715c284f93ddfb999897c9d92d55ed/bin/mmpbsa_py_energy failed with prmtop /tmp/tmp3slmqozl/files/000/dataset_18.dat!
Exiting. All files have been retained.
Ah, in the sander log:
FATAL: NATOM mismatch in coord and topology files
@chrisbarnettster: cool, I've got it working. Can we aim to get that PR merged this week?
this analysis of md is , MD done by NAMD, anyone guide me how to analyze MD trajectories with AMBER?
@tsenapathi convert to what???
Coordinates to pdb format
Need to change “Number of steps for the simulation”: 1000000 to 100000000
Hi @vmevada102 You can use the Galaxy production simulation tool. Under parameter input choose to upload your own MDP file or choose to use default. If you choose default there is a slider to choose the number of steps. Hope this will help. Some details of how to use GROMACS in Galaxy can be found at https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/md-simulation-gromacs/tutorial.html
As per the tutorial at here, https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/htmd-analysis/tutorial.html As per the instructions, it is only available at Production simulation step in Last step of Gromacs
@vmevada102 If your system is prepared and has been equilibrated then the production simulation tool is the correct one to use for publication ready simulations. It seems that the issue is that the “Number of steps for the simulation” parameter has a limit. You can either use an MDP file or you can run 100 simulations of 1000000 steps remembering to use the CPT file from the previous step. @simonbray:matrix.org any other suggestions for this usecase?
Hello @vmevada102, if you want to run a longer simulation, you need to upload an MDP file with this specified
The CPT files don't need any special treatment, you can just use those as described in the tutorial
However, i am unfortunate to get the results. As there is an error raised in the step.
error
An error occurred with this dataset:
This job was resubmitted to the queue because it encountered a tool detected error condition on its compute resource.
An error occurred with this dataset:
This job was resubmitted to the queue because it encountered a tool detected error condition on its compute resource.
Galaxy Tool ID: toolshed.g2.bx.psu.edu/repos/chemteam/gmx_md/gmx_md/2018.2
Command Line empty
Tool Standard Output empty
Tool Standard Error empty
Tool Exit Code: 1
Job Messages
{ "code_desc": "", "desc": "Fatal error: Exit code 1 ()", "error_level": 3, "exit_code": 1, "type": "exit_code" }
Job API ID: 11ac94870d0bb33aefea6162a0fcebba
Command Line empty
Tool Standard Output empty
Tool Standard Error empty
Tool Exit Code: 1
Job Messages
{ "code_desc": "", "desc": "Fatal error: Exit code 1 ()", "error_level": 3, "exit_code": 1, "type": "exit_code" }
Job API ID: 11ac94870d0bb33aefea6162a0fcebba
For example ...