Re: Tool for Repositioning disordered loop: TMD

From: Ashkan Shekaari (
Date: Wed Jan 26 2022 - 10:42:33 CST

k is too large,
it is conventional using smd instead of tmd

All the best,
Ashkan Shekaari

On Jan 24, 2022 20:31, Alexander Adams <> wrote:
Dear community,

I have a protein built from a crystal structure, with a mostly disordered loop that has been artificially generated. The loop is generated pointed in the +x direction, and I'd like for it to point in the -x direction. To achieve this, I used VMD to reposition the end residues to an approximate location and saved these modified coordinates.

From there I first tried running a minimization with the relocated end residues held fixed to see if the rest of the loop would be relaxed to the new orientation, but there were only small local arrangements, and the artificially stretched bond between the altered end residues and the original coordinates was unchanged.

Afterwards, I attempted to pull the end residues to the new coordinates via TMD. I placed strong harmonic restraints on 2 alpha carbons in the main body of the protein to keep the entire structure from simply translating, and then set the alpha carbons of my end residues for TMD to the new coordinates. When no progress was made over the course of 5 ns, I iteratively increased TMDk to the point where there was constraint failure, still without seeing an appreciable change in the coordinates. My TMD settings are as follows:

TMD                             on
TMDk                           2000
TMDOutputFreq           1000
TMDFile                        restraints/TMD_test.pdb
TMDLastStep                2500000

My questions: Is there a fundamental flaw in using these methods to achieve my goal, or is it more likely that the error is in executing the TMD simulation? If it's unsurprising that these procedures failed to produce the desired effect, is there a different method I should use instead?

Thanks in advance for your time,
Alex Adams
University of Michigan, Ann Arbor
Ph.D. Candidate - Mayes Lab
College of Engineering - Chemical Engineering 

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