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protein-DNA complex, DNA forcefield
- Sangeetha
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10 years 11 months ago #1566
by Sangeetha
protein-DNA complex, DNA forcefield was created by Sangeetha
Hi all,
I am working with a protein-DNA complex and I wish to run simulations for a longer time period. Hence I chose CG. Since I have a DNA, I am not able to use CG efficiently.
I have referred the paper by Khalid et.al. and has been using an elastic network model with 0.7 nm cut-off. But with this method the DNA does not show any conformational changes and is highly rigid.
With the recent release of martini2.2, I tried to simulate this complex.
With the help of Martinize 2.2 script, I generated the topology for the complex and while running with martini2.2.itp force field, I get an error saying that atom type SPd not found.
In the forcefield martini22dna, atom types for DNA bases DG and DC contains side chain beads of atom type SPd.
Is there any way to treat this atom type with martini2.2?
If not then when and where can I expect the martini22dna force field?
Thanks in advance
I am working with a protein-DNA complex and I wish to run simulations for a longer time period. Hence I chose CG. Since I have a DNA, I am not able to use CG efficiently.
I have referred the paper by Khalid et.al. and has been using an elastic network model with 0.7 nm cut-off. But with this method the DNA does not show any conformational changes and is highly rigid.
With the recent release of martini2.2, I tried to simulate this complex.
With the help of Martinize 2.2 script, I generated the topology for the complex and while running with martini2.2.itp force field, I get an error saying that atom type SPd not found.
In the forcefield martini22dna, atom types for DNA bases DG and DC contains side chain beads of atom type SPd.
Is there any way to treat this atom type with martini2.2?
If not then when and where can I expect the martini22dna force field?
Thanks in advance
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- jaakko
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10 years 11 months ago #1567
by jaakko
Replied by jaakko on topic protein-DNA complex, DNA forcefield
Hi Sangeetha,
there are no DNA parameters in the released martini 2.2. force field ( http://dx.doi.org/10.1021/ct300646g ).
We've added DNA to the martinize script for testing purposes only, it should give you a warning if you're trying to use the DNA part. Currently it is there only to make sure that the script reads DNA structures correctly and creates itp files for them that are of the correct format. However, and I need to stress this, the parameters it uses are just placeholders and one should not use them for any production runs.
DNA parameters are coming but they're not finished yet (you can blame that on me...). Can't give you any exact time frame when they're done, it's still a work in progress. Once they are done, they will show up here at the website and there's bound to be a news item on the front page that should be hard to miss.
Cheers,
Jaakko
there are no DNA parameters in the released martini 2.2. force field ( http://dx.doi.org/10.1021/ct300646g ).
We've added DNA to the martinize script for testing purposes only, it should give you a warning if you're trying to use the DNA part. Currently it is there only to make sure that the script reads DNA structures correctly and creates itp files for them that are of the correct format. However, and I need to stress this, the parameters it uses are just placeholders and one should not use them for any production runs.
DNA parameters are coming but they're not finished yet (you can blame that on me...). Can't give you any exact time frame when they're done, it's still a work in progress. Once they are done, they will show up here at the website and there's bound to be a news item on the front page that should be hard to miss.
Cheers,
Jaakko
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- gskinner
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10 years 3 months ago #3459
by gskinner
Replied by gskinner on topic protein-DNA complex, DNA forcefield
I am also looking to simulate protein/DNA systems. Is there any sort of ETA on when such parameters might be available? I am very much looking forward to trying them!
Best
Best
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- jaakko
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10 years 3 months ago #3463
by jaakko
Replied by jaakko on topic protein-DNA complex, DNA forcefield
Hi,
I'm hoping to have a beta version out within a month.
- Jaakko
I'm hoping to have a beta version out within a month.
- Jaakko
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- gskinner
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10 years 1 month ago - 10 years 1 month ago #3529
by gskinner
Replied by gskinner on topic protein-DNA complex, DNA forcefield
How is the progress coming along with the beta? I am happy to test!
Last edit: 10 years 1 month ago by gskinner. Reason: grammatical error
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10 years 1 month ago #3530
by jaakko
Replied by jaakko on topic protein-DNA complex, DNA forcefield
Hi,
the model has taken longer than I hoped to parameterize. I'm running now tests for the beta and hope to have it out in a week or two. It will still have an elastic network for double-stranded DNA so the kind of systems that require lots of flexibility the original poster was talking about should be treated with caution.
I will update the threads asking about it as soon as the beta is on the website.
- Jaakko
the model has taken longer than I hoped to parameterize. I'm running now tests for the beta and hope to have it out in a week or two. It will still have an elastic network for double-stranded DNA so the kind of systems that require lots of flexibility the original poster was talking about should be treated with caution.
I will update the threads asking about it as soon as the beta is on the website.
- Jaakko
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