I am also having trouble with the Gromacs initial setup. Galaxy… this is my history, please help me with this.
Welcome, @aczoo_rs_University
I stated up a fresh test of the GROMACS introduction tutorial workflow, but this time at the UseGalaxy.eu server.
That “answer key” history is running here → https://usegalaxy.eu/u/jenj/h/gromacs-training-workflow
I’m looking at your history next. The usual problem is missing required data in the input PDB file, but I’ll check to see what I notice. More soon and thanks for sharing the history with your question! Super helpful. 
Yes, the guess was right: the problem is with the PDB record content. It isn’t complete enough to use for this.
If you are curious about what exactly is missing, review the filtered record (dataset 2). The headers described the processing for each, and your file also has notation about what is missing. You can compare to the headers in the example record, too.
For later, for you or anyone else reading: The GROMACS tutorial workflow can be adapted to retrieve and load up any PDB record. Use the links to import the workflow, click to expand the steps, and edit the record identifier in the first step, then start it up. This is very quick way to get data loaded. From there you can apply custom manipulations.
Hope this helps!
Thank you@jennaj. is this are taking about??
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
If it is this?? how should I correct it?? thanks in advance.
I don’t think that you can correct this, the author who submitted the record would instead need to provide it, maybe in an update. You could try to contact them.
The other option is to try to find and use a more complete record for this molecule, if it exists already…
SO … there isn’t a good solution, and that would be true wherever you are using GROMACS. If there is no useable data, there is nothing to simulate.
hi@jennaj, should I use another PDB file, the last one I extracted from RCSB… should I download it and prepare it in Pymol, chimera or Maestro. and rerun in galaxy??
I’m not sure familiar with this analysis domain … mostly just the usage and some basic data interpretation. So, let’s ask anther moderator who is a scientist that worked on these tools. 
Hi @wm75 would you be able to help or suggest someone who could? I would be interested in the answer too, since this comes up every so often (poor content PDB data) and don’t know of a good solution beyond locating better public data.
Hi, @jennaj, @wm75 Galaxy
I have used PDB fixer which seems to have solved the setup problem, but it still needs some technical adjustment, now the problem appears to be solved, I am trying to optimize the PDB fixer so that it runs smoothly. Please correct me if I am wrong.
@aczoo_rs_University PDB fixer is for sure worth a try.
In general, @simonbray would be a good person to ask about this entire topic. Let’s see if he is around.
I would also like to share this
The Gromacs simulation tool is also not running after Gromacs energy minimization.
@jennaj @simonbray
Thank you in advance
GROMACS simulation tool is not running after GROMACS energy minimization
here is my history link Galaxy ,
also why my comments are getting flagged?? @jennaj
Let’s merge your question in the new thread with this one. Try to post just once: we’ll see it. The people who are helping you are other scientists.
Thank you @jennaj. I am hoping for a solution soon.
Dear, @jennaj , I think the tool ‘GROMACS simulation for system equilibration or data collection(Galaxy Version 2022+galaxy0)’ is non-functional, it is more of a software issue than a technical one. The problem is after loading the previous output file from GROMACS energy minimization (Galaxy Version 2022+galaxy0) to GROMACS simulation. it is taking all the inputs, but when the run button is clicked, it shows no response. Please help me out in this.
Regards.
Are you still having this problem?
If a tool will not submit, that (usually) means that a required input was not selected. You’ll see a light blue highlight around the missing option/data. Once that is resolved, then you’ll be able to submit.
Maybe share a screenshot? The idea is that we can try to match up the exact data in the history you are trying to submit, to try to reproduce this. I tried using your description + history but everything seemed Ok to me… but I maybe didn’t do this exactly the same way you were!
If there is a software problem instead of a data problem, this is also how to report it. Then we can sort it to the right people to get a fix.
I checked both your shared histories and neither is the same as the history in your screenshots. If you want to share that history I’m still willing to take a look. And if you solved this already, you can let us know. Thanks! 
1 Like
Dear @jennaj. I have run two different PDB files, one shown in the tutorial by Simon Bray, which runs fine as PDB files no need of PDB fixer. Here is the 1st link & screenshots Galaxy
sharing the second one in the next reply within a few minutes.
Thanks @aczoo_rs_University
I see the problem: open up the section for Settings and you’ll see the blue box (required for the types of outputs selected). There is a “partially default” choice, or an MDP file would go here.
Now, it would certainly be nicer if that was much more obvious but sometimes it is difficult to model so many different dependent parameters in a way that works for all combinations. The best advice I have is to open the options, and you’ll find that blue box somewhere.
The EU team will see our conversation… and they work on these tools, so maybe this will be improved in the future. But if you feel strongly about getting some kind of change in place, or a specific change, please open an issue ticket against the development repository explaining what you would prefer happens instead. Maybe it can happen! Tool form → Options → See in ToolShed → Development link.
Thanks for following up and let us know how that works!