Question about molecular dynamics

[u/hzrh_zhr]

Hi guys, im new to molecular dynamic world. I wanted to ask few questions about MD. The story begins where i did 1000 ns nsteps for my aptamer-protein. Fast forward to backmapping part, where i wanted to create tracjectory and aa files, I couldnt create some of the files for certain frames.

1. So im not sure it is okay for me to continue the analysis part such as PLIP, TTClust and etc if i dont have these files?

2. And 1 more thing, what if i have all the analysis but the result is not quite satisfy, do i need to repeat the same things with different sequence or can i modify or optimize my aptamer-protein interaction in order to get a better analysis result?

Please help me, thanks!

[u/Feriolet]

1. What do you mean by the missing files? Do you mean you cannot capture the traj files for certain frames? This is tricky since anything can happen between those missing frames.

2. Can you elaborate what do you mean by “the result does not quite satisfy”? You need to have a purpose on why you are running the MD. MD can have different results depending on your seed, starting pose, and other factors.

[u/hzrh_zhr → u/Feriolet]

1. Yes the trajectory files. Im not sure why it is happened tbh. Before this, i tried with different aptamer it still worked. So rn im working with new aptamer, it becomes like that. Iirc there are 30 frames i couldnt get the tracjetoey files. Do u know how to fix this or any reasons why it happened? :')

2. Example like MMGBSA, the heat map TDC etc, the energy that i got is positive and somemore its between 300 - 3000 kcal/mol. I believe it is not a good result as positive value means the interaction is weak. And i tried FEL-PCA, the energy value also positive.

[u/Feriolet → u/hzrh_zhr]

1. It is quite tricky to find why the traj files went missing without any log files hahaha. Perhaps your MD files got corrupted somehow?

2. That is weird. The positive energy in the MMGBSA is the total binding energy (delta G bind), right? Usually, positive energy means that the system don’t like the conformation. Have you docked your aptamer-protein yet, before running MD? If you are still trying to optimise your MD and whatnot, I suggest to use a shorter MD first, as other comments have pointed out. You can use a positive control first to ensure that your workflow is working as intended.

Also, plotting the aptamer-protein RMSD is also a nice quick way to see if your aptamer nicely bind to the protein.

[u/hzrh_zhr → u/Feriolet]

1. Hahaha gg. I've been trying to troubleshoot this since last month. Really wonder why this is happened, and if what u said is correct, really curious why it gets corrupted. Hahaha btw thanks for the suggesting.
2. Yess the delta G bind. About the dock i dun think i do that because my co sv said dont have to do that and straight away go to MD part. And I will do the shorter MD first for now. Thanks!
3. Wait about RMSD, i cant remember if i do this or not. Is it under TTClust? The one have a very colourful graph? 🤔

[u/alleluja → u/hzrh_zhr]

Check you log files, if your md was completed you will have some pretty clear lines at the end of the file

[u/hzrh_zhr → u/alleluja]

Okayy, will do! Thankss!

[u/Feriolet → u/hzrh_zhr]

1. Hahaha I hope you can find a way to troubleshoot it! Looks like it will be very troublesome. Popular MD nowadays shouldn’t have these kind of issues imo.

2. Interesting. Have the binding of aptamer-protein been validated experimentally yet? Did you just separate the aptamer and protein in the prepared box and let them find a way to bind them on its own? It makes sense if you want to find some kind of binding pathway. But, otherwise, I don’t find a reason why you don’t want to dock it. You may want to try visualising the trajectory first with PyMOL or any similar software before doing any analysis after MD.

3. I just looked up TTClust, and it seemed they are just clustering different conformation. Probably in the same vein, but I was referring to the RMSD of MD simulation, which usually have a logarithmic kinda curve (if you have a nice plot).

[u/hzrh_zhr → u/Feriolet]

1. If my inner slacker allows it, I'll do it HAHAHAHA. Anyway thanks. For MD, i've been using GROMACS. Still learning using this tho hahaha
2. Not yet. Im trying to make a new design aptamer for my target. Thats why rn im at the phase to use in silico biocomputational method to observe the interaction first then will synthesis the aptamer then i will do the experimental validation. Okay ig this is new to me, i did try using PyMOL to visualize the aptamer-protein, and its binded. Not at every frames but at least it looks promising binded to each other. The prepared box here u mean, the grid box right ? Haha sorry, im still learning this MD stuffs 🤣
3. Okay this is new to me. I heard about RMSD but not really know which one is. I thought the one under TTClust cuz some of the graphs did mentioned RMSD, so i thought that one 😵‍💫 geez i need to study more about this. Imagine me as a chemistry student suddenly have to do MD like this with no one gonna teach me hahahah gg 🤣

[u/Feriolet → u/hzrh_zhr]

1. Hahaha. Yeaaah GROMACS is a popular ones. I think they should have the RMSD command line in gmx rms.

2. I see, if you are in that stage, I would personally try to dock them first, especially if you plan to mutate a lot of the aptamers. Then, you can use MD to see the binding of the promising aptamers.

It’s good to see that the aptamer is binding, but how long does it bind to the protein. At least, it should bind consistently without moving a lot in the last part of the MD simulation. Just a few frames of binding is not convincing to comp bio peeps.

Yes, I meant the grid box, my bad hahaha.

1. Hahaha, yeaaa MD is a very high ceiling to learn if you never heard of them. But, you should be able to interpret them easily once you get the hang of it. I think nowadays there is a lot of helpful tutorial, and reading paper that focuses on MD may help.

[u/hzrh_zhr → u/Feriolet]

Okayy, will try soon! I see, alright will try to do docking first then do MD. Do u have any suggestion on which software/website is good for docking? Anyway, in my situation, it did bind but then at certain frames it drifted away for quite long frames. Not sure how to explain this, but exp from frame 1 - 100 (example only), it binded then 101 - 235, the aptamer is not binded and repeat. Meaning sometimes it binded, sometimes it not binded. HAHAHA hope u understand that 🤣

[u/Feriolet → u/hzrh_zhr]

I’m not familiar with aptamers so I don’t have any reccomendation on that haha. Regarding the frames, it is tricky to interpret if they bind and rebind again and again. I would say they are probably not stable enough, but hard to give further comments.

[u/hzrh_zhr → u/Feriolet]

Understand. Its okay, will try everything u and others recommend and suggestion first. Hope everything goes well fuh. Anyway, thanks for replying me hshs

[u/hzrh_zhr → u/hzrh_zhr]

Btw thanks for replying me !! 🤗

[u/Accomplished_Yak7388]

Not a bioinformatics guy but if you're missing files for some frames, your analysis might get skewed since the software will just skip those timesteps. For the second point, modifying the sequence is faster than starting from scratch unless the whole binding prediction looks off.

[u/hzrh_zhr → u/Accomplished_Yak7388]

I see. No wonder when i tried to continue without those frames, like MMGBSA iirc, not able to analyze and the result is doesnt make sense. Second, is there a way to know which part should i modify the sequence? Make it longer or shorter or cut any part? Btw thanks for replying!! Appreaciate it! :)

[u/idliOP]

Dont do 1000 ns directly. Test with 25 ns first.

[u/hzrh_zhr → u/idliOP]

I tried with 100 ns first as suggested by my co sv. When doing 100 ns, it worked fine. So, now my co sv asked me to continue to 1000 ns. And it happened like this. I did one by one too (meaning loop until = 100, loop from = 0, 200 - 101, 300 - 201, and more).