DNA modeling in MMB

Divita Mathur · Post by **Divita Mathur** » Tue Mar 05, 2013 1:55 pm

Hi
Firstly, I must commend the team on the fantastic tutorial. It is clear, to the point and covers possible errors and solutions.
I am trying to use MMB to model DNA sequences with certain base interactions (baseInteraction B 2 WatsonCrick B 6 WatsonCrick Cis). However, I am running into this error ( Unable to find parameters for interaction : baseInteraction between residue type: "DG " , and residue type "DC ", parameter WatsonCrick, WatsonCrick, orientation Cis between residue numbers 2 and 6). I'm assuming it's because MMB is adding 'D' before all the bases and is unable to find the parameters in parameters.csv.

Could you tell me why this is happening and what the solution is?
Thanks much!
Divita

Divita Mathur · Post by **Divita Mathur** » Tue Mar 05, 2013 2:34 pm

Oh, and I don't face this problem when I use 'loadSequencesFromPdb' to load sequence.

Samuel Flores · Post by **Samuel Flores** » Fri Mar 08, 2013 9:08 am

What operating system are you on? I have just fixed this bug in the 2.11 OSX release. The releases for other operating systems are not yet updated.

Turns out part of the problem was that parameters.csv did not contain the parameters for DG, DU, DC, and DA bases, as you intuited. It did have them for G,U,C and A, which are not the official PDB-supported 3-letter residue types. I also had to change some things in the source code which referred to these residues as G,U,C,A.

Anyway, if you're on OSX just download 2.11. Otherwise, what OS are you using?

Samuel Flores · Post by **Samuel Flores** » Wed Mar 20, 2013 2:22 am

I've just updated MMB 2.11 for windows, which fixes this problem . please re-download it now and let me know if it works for you.

sam

DNA modeling in MMB

DNA modeling in MMB

Re: DNA modeling in MMB

Re: DNA modeling in MMB

Re: DNA modeling in MMB