Position restraints error !!!

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1

Hello Everyone. So, after completing all the steps for MD, I am still getting these errors. any ideas on how to fix these. It would be really helpful since I am a newbie in MD simulation.

NOTE 2 [file ./md.mdp]:
Removing center of mass motion in the presence of position restraints
might cause artifacts. When you are using position restraints to
equilibrate a macro-molecule, the artifacts are usually negligible.

NOTE 3 [file ./md.mdp]:
This run will generate roughly 24373 Mb of data

2

Hi @Siam_Siraji

Could you provide more context please?

  1. Which Galaxy server are you working at? URL please
  2. Which tutorial are you following? What step are you having problems with? URL please to the tutorial, and a the full tool name + version (find this at the top of each tool form)
  3. What do the job logs state (stderr + stdout) or is that what you posted?
  4. A screenshot might be helpful if it is part of the output display
  5. If you are able to share a link to the history, and note the error dataset #, that would also be helpful

FAQs:

3

Hello, Thank you for the reply.

I am using Galaxy European server (Galaxy Version 2022+galaxy0)
I am following the tutorial ‘GTN Training - Computational Chemistry - High-throughput Molecular Dynamics’ on youtube.

in this job, I tried to run the MD for my own docked protein-ligand complex.

Here is the History link. Galaxy | Europe | Published History | Vibrio 5gvz

Please let me know how can I fix these error datasets I am getting. I am a newbie in terms of MD. So it would be really helpful for me.

gromacs
gromacs1171×553 20.3 KB

1 Like
4

Hi @Siam_Siraji

It looks like the data problem was introduced at the data preparation step where the proteins and ligands were separated + manipulated here.

The ligand was filtered with the wrong keyword. Should be “AG5E” and not “UNL”.

screenshot1
screenshot1886×430 31.4 KB

The protein filter was correct, but the next manipulation “Set up protein topology” on that output didn’t output the complete report. This option should be true “Generate detailed log”.

screenshot2
screenshot2868×308 20.1 KB

Fix those, then redo the downstream steps.

How I found this:

  • By comparing the “job details” page for the datasets (found under the :information_source: icon within the expanded datasets) to the tutorial instructions. This is a simpler view of the parameters actually submitted for a job.
  • I usually start by reviewing the error dataset, and if I can’t see an obvious problem, then go back and review all the upstream steps from the start. But you can decide what order to do this when checking your own work.
  • FAQ troubleshooting-errors
5

Thanks again,

But I think the name for my ligand is UNL, not the AG5E. The ligand is my own. I am not using the tutorial ligand.

6

Hi @Siam_Siraji

Ok – I missed that! If you think that the steps leading up to the failure are correct, the problem could be content versus parameters.

I’m also wondering if the job is simply running out of resources. This prior QA Tool error in protein-ligand md simulation in Gromacs failed for exceeding resources with “WARNING: This run will generate roughly 3843 Mb of data”. Your job is significantly larger with 13562 Mb of data.

The first warning (Note 1) indicates you could optimise the “Bond constraints (constraints)” setting to better fit your data. I’m not sure if changing that will address the second warning (Note 2) or not but you could try a test run. And, you could also try the advice from the other Q&A – lower the steps to check if a smaller job runs or not at the public site with the allocated resources.

Let’s also pull in help from one of the tool wrapper authors, ping @simonbray.

7

All right, Thanks for the suggestions.

I am submitting the job again. Let’s see what happens.