Hi sam, This MD run was not meant to be informative, but was just a debugging step just to ensure that any molecule fed into MMB retains proper sterochemistry. For all my scripts, i found this was not the case. I suspect i am missing out on a few crucial commands or failed to understand how certain ...

Hi sam, I am not running MD, but i have been trying to run some homology modelling, but the insertions and base pairs are not properly preserved nor is their structure 'reasonable' after quick visual inspection. I ran this 'MD' step just as a debugging step for MMB and i found the forcefield or time...

Hi Sam, I was doing an MD run, but it has exploded. For speed purposes, i rigidified most of the RNA, but kept residues 51-69 free and included default MD parameters for these residues and a few others more. However, the MD run was exploding. Is there a way to reduce the time step ? I started from a...

Thanks for the references.

Xiong An

I have got a question, what is RNA threading and morphing. MMB uses these methods for modelling RNA, but googling more about these method nor publications of RNAbuilder did not find any formal introduction or definition of threading nor morphing.

Xiong An

nucleicAcidDuplex will work with the force field turned on, but you have to do two things: 1. Make sure the base pairing forces are strong enough. You can increase them by 100 or 1000x just to test. 2. Make sure the MD forces are turned off for the template. I am afraid you will probably have to pl...

Yes, i was trying to validate homology modelling with insertions, a validation example is the SAM riboswitch. There are three different loop lengths in PDB structures, though all share a similar core aptmer. It is shown in the picture below. For purposes in the post, i shall call them small, medium ...

Thanks Sam for your very prompt reply and concern :D ! I elaborated more on my problems below ! yes, the inserted residues are treated like any other residues. So you can apply base pairing forces to them. I used commands nucleicAcidDuplex or baseInteraction C 26 WatsonCrick C 13 WatsonCrick Cis, bu...

Hi Sam, I got two questions. Firstly, is it was possible to insert secondary structure information onto the insertions. Secondly, while using MMB builder, there were some criss-crossing of the structures, are there any ways to correct these? Xiong An * Trival bug in linux version The excecutables in...

Hi Sam,

I am using MMB to model some RNA (TPP riboswitches), trying a few tools here and there. There are large insertions compared to the template, so this has to be taken in account
Thanks for the very prompt reply!

Xiong An