Re: Tool for Repositioning disordered loop: TMD

From: Alexander Adams (
Date: Thu Jan 27 2022 - 04:07:07 CST

Hi Hemanth,

Thank you for your advice. I did use VMD to reposition a portion of the
structure to the desired configuration, but I have not been able to relax
the remainder of the structure to the new coordinates, either by
minimization of the new structure or via TMD to pull towards the
coordinates generated in VMD.


On Wed, Jan 26, 2022 at 7:37 PM Hemanth Haridas <>

> 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
> origin.
> 3. Now issue the command set rot [set transaxis z 180]
> 4. Now rotate the selection using $sel move $rot
> Regards,
> Hemanth
> 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

University of Michigan, Ann Arbor
Ph.D. Candidate - Mayes Lab
College of Engineering - Chemical Engineering

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