DNA modeling in MMB
Posted: 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
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