normal Missing beads def in force field for ribonucleoproteins

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1 month 1 week ago #8253 by daniloboskovic
Dear caretakers,

I have recently found out that martini have missing beads for RNA in the combined particle force field file. I have read the paper on RNA-protein interactions and i have taken the fact that martini works for ribonucleoproteins as granted. But as i tried to do a simulation i have realized that the topology file has missing definitions for RNA beads. I am on quite a busy schedule for the next two weeks and am supposed to do at least one simulation by the end of it. If you can step up and help me out in solving this problem would be very much appreciated.

Thanks,

D.B.

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1 month 6 days ago #8254 by peterkroon
Hi DB,

I assume that you tried to make the ITP file for you protein using martinize, and that the RNA part of your protein didn't end up in the final ITP.
Unfortunately, this is expected behaviour.
We are working on a new tool (martinize2) that should address these cases, but you'd have to do some work to get it to work for your system.
Since you're on such a tight deadline, I suggest you martinize the protein and RNA parts separately, and combine them by hand. You'll have to look up the bonded parameters linking the protein and RNA; and whether there should be an elastic network between them.

Good luck!
Peter

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1 month 6 days ago - 1 month 6 days ago #8255 by daniloboskovic
Replied by daniloboskovic on topic Missing beads def in force field for ribonucleoproteins
Dear P. Kroon,

Thank you so much for your quick answer. I already combined the two as i too expected that behavior. In my simulation i have two separate molecules added randomly in a box (protein and RNA, once each) and i want to see their interactions without elastic network. When i run the simulation i got an error that atomtype TN0 is not found. It will be fine if i just get the simulation of an RNA and a Protein to run for now. Upon further investigation i realized that TN0 is only defined in martini_v2.1-dna.itp but not the martin_v2.1.itp which caused the error (among other potential errors from undefined parameters of beads) and that combining the two wouldn't exactly solve the issue (nor adding both in the top file). If you, or another caretaker that has time, could give me an advice regarding this i would be very grateful!
Last edit: 1 month 6 days ago by daniloboskovic.

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1 month 6 days ago #8258 by peterkroon
As far as I can tell you should simply use martini_v2.1-dna.itp. The parameters in there (I checked a few) are the same for those in martini_v2.2.itp, but they're defined as sigma and epsilon, rather than as V and W.
To check: take a gro file with a protein in water, prepare tpr files with both itp files, and check the potential energy.

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1 month 6 days ago - 1 month 6 days ago #8259 by daniloboskovic
Replied by daniloboskovic on topic Missing beads def in force field for ribonucleoproteins
Ok. Thanks. I guess that is what confused me as my background is not in bioinformatics. Thanks once again! Seems like i will make it!
Last edit: 1 month 6 days ago by daniloboskovic.

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