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Questions and answers => MD simulations => Topic started by: vito_genna on October 13, 2013, 10:00:20 am

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Title: DNA screwing into protein
Post by: vito_genna on October 13, 2013, 10:00:20 am

Hi to all users,
I have started to use 3DNA yesterday. I have to say that 3DNA is a powerfull tool to analyze different and various kind of usefull parameters.
I've run the rubi_script to analyze my trajectories and it works really nice. Just to clarify, I would to suggest you to use TRJCONV (only this)
to convert your trajectories file in a .pdb list, otherwise, the same output will not work properly if you use catdcd or another converter.

Now i would to ask your opinion.
I would to study which is the rotation angle value of my whole DNA molecule that is in complex with a protein.
basically I'm studying Polymerase, WT and Mutated one, to evaluate if that residue is really involved in.
Whit the twist parameter i can't study it.
Someone have any suggestion?

thanks in advance.

Best regards

Vito

Title: Re: DNA screwing into protein
Post by: xiangjun on October 13, 2013, 03:13:58 pm

Hi Vito,

Thanks for your kind words about 3DNA, and for sharing your experience on converting MD trajectories file to PDB format.

Quote

I would to study which is the rotation angle value of my whole DNA molecule that is in complex with a protein. basically I'm studying Polymerase, WT and Mutated one, to evaluate if that residue is really involved in. Whit the twist parameter i can't study it. Someone have any suggestion?

I am not quite sure what do you mean by "the rotation angle value" of your whole DNA molecule. Overall, it'd be case-specific as how to quantify changes in relative orientation between DNA molecules in wt vs mutated complexes. The 3DNA algorithm for calculating the base-pair step or helical parameters may be applicable, with a proper definition of coordinate frame.

Xiang-Jun

Title: Re: DNA screwing into protein
Post by: vito_genna on October 14, 2013, 08:42:15 am

Dear Xiang-Jun,

I would to consider my DNA like a cylinder inside the protein and i would to study how this cylinder rotate referring to the protein.
I'm writing my own script to measure it.
Thank you for your fast reply.

Best Regards

Vito

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