3DNA Forum

Questions and answers => RNA structures (DSSR) => Topic started by: hijibijbij on April 03, 2018, 07:58:19 am

Title: Centre of Mass Pseudodihedral Angle
Post by: hijibijbij on April 03, 2018, 07:58:19 am: Hi,

I have a silly question. I am very new in this field, I am trying to simulate a RNA structure. For that I need to measure the CPD (Centre of Mass Pseudodihedral Angle) angle of RNA. But some how I am not getting it in dssr-torsion.txt. Can anyone please suggest how to find it or how to calculate it
Thank you in advance
Title: Re: Centre of Mass Pseudodihedral Angle
Post by: xiangjun on April 03, 2018, 08:33:33 am: Hi,

Could you please let us know what exactly is “CPD (Centre of Mass Pseudodihedral Angle)”? Please also provide worked example so I can understand how to calculate it from atmoic coordinates.

Thanks,

Xiang-Jun
Title: Re: Centre of Mass Pseudodihedral Angle
Post by: hijibijbij on April 03, 2018, 11:10:11 am: i am talking about COM pseudo dihedral angle, a restraint co-ordinate for doing umbrella sampling. here we restraining COM of two sugar molecule above target base, one sugar molecule below of it and the target base. For further understanding you can see the attachment.
Title: Re: Centre of Mass Pseudodihedral Angle
Post by: xiangjun on April 03, 2018, 11:29:30 am: Thanks for your followup. Now I can understand your original question a bit better. So COM stands for "center of mass" based on the attached figure caption. I still do not know what "CPD" stands for.

From the attached figure, it is still not clear to me what the two sugars above the target base are. Do the corresponding bases (attached to the sugars) must form a Watson-Crick (WC) pair? Do the three nucleotides where the base is in the middle must be consecutive in sequence?

Based on my understanding, I do not think adding this pseudo torsion angle (θ) is a good fit for DSSR (at least at this stage). See my post titled "Request for new features" (http://forum.x3dna.org/feature-requests/request-for-new-features/).

Why not ask for help from the author who defined this parameter? If that does not work out, you may write your own code or hire someone with basic programming skills for this purpose. Assuming the structure is a double helix with WC pairs, it should not be a big deal.

Xiang-Jun