normal RNA helix

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3 weeks 2 days ago #8004 by dariush
RNA helix was created by dariush
Hello,

I set up a system containing double-stranded RNA in a helical form using 50G and 50C. After converting this clean helix to CG and running the simulation for 200 ns usign stiff elastic network, I observed that the helix was deformed massively. I'd like to know why this happens. I talked to RNA experts. They believe RNA helix should be as stable as DNA helix and should tolerate forces to some degrees. Here I only ran 200ns in NPT at 300 T.

Herein please find the initial and final confs.
www.dropbox.com/sh/l7a01t4xnoypyz9/AAA9_...FlmxJ-MXHRXenra?dl=0

Thanks!
Dariush

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3 weeks 1 day ago #8005 by ifaustino
Replied by ifaustino on topic RNA helix
Hi Dariush,

Indeed the RNA bases seem to stack and deform the helix. Without knowing the martinize command was used to create the CG structure, my first guess is that the elastic network between the complementary bases is missing. Could you copy here what you used? Can you check the elastic network?

Ignacio

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3 weeks 1 day ago #8013 by dariush
Replied by dariush on topic RNA helix
Hi Ignacio,

Here is the command I used:
python martinize-nucleotide.py -type ds-stiff -f XX.gro -o cg-XX.top -x cg-XX.pdb -v

and here is the link to gro file I used. I convert pdb to gro using editconf and then ran the above command.

www.dropbox.com/s/0jhlktc987qe930/gc_duplex.gro?dl=0

Thank you for your help!
Dariush

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2 weeks 5 days ago #8014 by dariush
Replied by dariush on topic RNA helix
And here is the .itp file:
www.dropbox.com/s/5qdhj6coo1qno3g/Nuclei...2BNucleic_B.itp?dl=0

Thank you for your help!
Dariush

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2 weeks 3 days ago - 2 weeks 3 days ago #8015 by ifaustino
Replied by ifaustino on topic RNA helix
Hi Dariush,

Sorry for my delayed reply.
After checking your .itp file I realized the elastic network is missing, which explains your results during the MD simulation. I have been playing with the martinize-nucleotide.py version in the tutorial and I realized there is something odd when it builds the elastic network. While I make a corrected version of the script available in the tutorial files, I have made a new Nucleic_A+Nucleic_B.itp file that includes the elastic network.

drive.google.com/open?id=11d3TaMi4ZJanm_BEja7LD0QqD25v1yFb

Please check that this one works and let me know if you need other systems to simulate. I can assist you generating the .itp files.

Hope it helps,
Ignacio
Last edit: 2 weeks 3 days ago by ifaustino.

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2 weeks 3 days ago #8016 by dariush
Replied by dariush on topic RNA helix
Hi Ignacio,
It seems I don't have permission to open the link. Could you please change the permission or share it via a different method?

Thanks,
Dariush

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1 week 2 days ago #8032 by dariush
Replied by dariush on topic RNA helix
Hi Ignacio,

Below please find the final configuration after 200ns. I was expecting the helix stay stable, but it underwent a massive conformational change. Could you please let me know your opinion?

www.dropbox.com/s/85lo1a7k3nnzhzi/after_fix.png?dl=0

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1 week 1 day ago - 1 week 1 day ago #8033 by ifaustino
Replied by ifaustino on topic RNA helix
Hi Dariush,

Thanks for sending the pic.
Could you tell me whether you have the '#define RUBBER_BANDS' active in the .top or .itp file? It seems the elastic network is not ON.

Thanks,
Ignacio
Last edit: 1 week 1 day ago by ifaustino.

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1 week 1 day ago #8035 by dariush
Replied by dariush on topic RNA helix
Hi Ignacio,

I had assumed it'd be automatically on like proteins with the elastic network.
Anyways, I added '#define RUBBER_BANDS' to the .top file. It's working perfectly!!

Thanks! -Dariush

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