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    Anamika
    @anamika-8
    but i am not able to download
    Anamika
    @anamika-8
    Screen Shot 2021-03-08 at 3.20.32 PM.png
    I am getting this error.
    Simon Bray
    @simonbray
    I cannot really help you with installing VMD, sorry
    You can also try nglviewer which doesn't require a download: http://nglviewer.org/ngl/
    Anamika
    @anamika-8
    Thank you so much Sir for your help.
    chrisbarnettster
    @chrisbarnettster
    @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"
    Simon Bray
    @simonbray
    @chrisbarnettster I've been having some problems recently with the mmgbsa tool that you wrote. I keep getting errors like this Found an invalid periodicity in the prmtop file: 6
    simonbray
    @simonbray:matrix.org
    [m]
    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?
    chrisbarnettster
    @chrisbarnettster
    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I made some progress in the draft PR galaxycomputationalchemistry/galaxy-tools-compchem#75 which is now out of date and needs work.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.
    Simon Bray
    @simonbray:matrix.org
    [m]
    Thanks @chrisbarnettster - I'll check out your branch locally and try rerunning the tool
    chrisbarnettster
    @chrisbarnettster
    Happy to help to resolve this over the course of this week. We can chat via PR's in GitHub and/or on Gitter. :)
    Simon Bray
    @simonbray:matrix.org
    [m]
    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
    Simon Bray
    @simonbray:matrix.org
    [m]
    I'll try and fix that
    chrisbarnettster
    @chrisbarnettster
    đź‘Ť
    Simon Bray
    @simonbray:matrix.org
    [m]
    @chrisbarnettster: cool, I've got it working. Can we aim to get that PR merged this week?
    bgruening
    @bgruening:matrix.org
    [m]
    @simonbray: can you rebase this PR
    Simon Bray
    @simonbray:matrix.org
    [m]
    yes, working on it - I'm going to push a few commits as well
    bgruening
    @bgruening:matrix.org
    [m]
    Thanks!
    chrisbarnettster
    @chrisbarnettster
    @simonbray:matrix.org yes :)
    NomiDogar
    @NomiDogar
    hello everyone,
    this analysis of md is , MD done by NAMD, anyone guide me how to analyze MD trajectories with AMBER?
    Tharindu Senapathi
    @tsenapathi
    Hello @NomiDogar try to convert your trajectory and coordinates using our MDTraj file converter
    NomiDogar
    @NomiDogar
    anyone , AMBER user here?
    @tsenapathi convert to what???
    Tharindu Senapathi
    @tsenapathi
    Trajectory to dcd format
    Coordinates to pdb format
    NomiDogar
    @NomiDogar
    and then i can follow this tutorial??
    Tharindu Senapathi
    @tsenapathi
    Yes
    NomiDogar
    @NomiDogar
    ok thank you, i'll do that
    Tharindu Senapathi
    @tsenapathi
    Great đź‘Ť let us know if you need any help
    NomiDogar
    @NomiDogar
    sure
    vmevada102
    @vmevada102
    Need help to change the Gromacs simulation to run for 100 ns. As per the instructions, we can change via CPT file. But, i am not able to process it via uploaded cpt file
    Need to change “Number of steps for the simulation”: 1000000 to 100000000
    chrisbarnettster
    @chrisbarnettster
    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
    vmevada102
    @vmevada102
    Thank you for your reply @chrisbarnettster, i need to run this steps for publication purpose at 100 ns in Gromacs simulation step for Protein-Ligand complex. Does the suggestion provided by you sufficient?
    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
    chrisbarnettster
    @chrisbarnettster
    @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?
    Simon Bray
    @simonbray:matrix.org
    [m]
    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
    vmevada102
    @vmevada102
    Hi @simonbray:matrix.org as we can upload the mdp file for custom steps. I had uploadded the md.mdp file in the Gromacs Production Run step.This mdmdp file is as per the tutorial available on Gromacs Wesbite.
    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.
    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
    Jacqulene
    @jacqulenexp_twitter
    Hi where can I find the RMSD analysis tool?
    For example ...