Re: Tool for Repositioning disordered loop: TMD

From: Hemanth Haridas (
Date: Wed Jan 26 2022 - 21:37:11 CST

If you just want to reorient the structure, you would be better off trying
VMD, where you can use the following commands to get the job done.

1. Create a selection of the segment that you want to reorient using set
sel [atomselect top "your selection"]

2. Then translate it such that the COM of the selection corresponds to

3. Now issue the command set rot [set transaxis z 180]

4. Now rotate the selection using $sel move $rot


On Mon, 24 Jan 2022, 22:34 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
> --
> (he/him/his)
> University of Michigan, Ann Arbor
> Ph.D. Candidate - Mayes Lab
> College of Engineering - Chemical Engineering

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