Hi Adelene,
You’re right, the example threads a little messily. I’ve fixed this for the next release (2.16). I made the following changes:
1. Threaded to one additional residue on the template.
2. Used “physics where you want it” rather than the contact command to prevent steric clashes. This will spread out the loop nicely, and is just better all around (uses PARM99).
3. Shifted the template so it’s less likely to tangle. There are other ways to get out of kinetic traps, but for a simple example I thought we’d go this way.
4. Shortened the simulation time. You don’t need to run for 500 steps.
I’ve attached the updated PDB and command file.
Sam
On Dec 9, 2014, at 10:56 PM, Adelene Sim <adelenes(a)bii.a-star.edu.sg> wrote:
> Hi Sam,
>
> I'm having some trouble with threading on MMB and was wondering if you can help me take a quick look. Basically I'm following the tutorial and trying to do RNA threading. Turns out my RNA doesn't look right and there appears to be lots of clashes even though I followed the tutorial's input. I tried to run for longer just to see if it'll equilibrate but sadly it didn't!
>
> The input, output and final trajectory file can be downloaded from here: https://www.dropbox.com/sh/tx9hpvw772h3hz0/AABnj-_n0lAbLijD9ZLBJwz4a?dl=0
>
> From looking at the trajectory it appears as if the sterics component is not implemented and the RNA gets very distorted. I used the Mac binary downloaded from SimTK.
>
> I know you're busy so I really appreciate it if you can take a look! Thanks!
>
> Adelene
>
> On 25/11/14 6:23 AM, Samuel Flores wrote:
>> You have been contacted by a member of Simtk.org.
>>
