I am trying to model the transition of a segment within protein using a starting point, an end point, and some intermediate structures with coarse-features.
Specifically, I have a starting structure (all-atom), and ending structure (all-atom), and several intermediate coordinates (only Ca backbone atoms).
I remember years ago I was able to use AMBER and targeted MD to move the full-atom coordinates until the relevant atoms fit over the coarse-grained coordinates, but I do not remember now, and I had to change institutions a while ago and misplaced the relevant pieces of code.
Does anyone know how it can be done?
Thank you.
If you are familiar with NAMD, I can give you some initial scripts to modify.
This is a script for 50 ns TMD simulation, where the driving forces are applied only in the first 25 ns. The force is very high since my system was too big and I was just trying to see the conformational change within 25 ns. I suggest using TMDk=200 instead of 20000 but it all depend on your system, your hardware, how much transition you want to see etc. You will have to prepare a pdb file called "
tmd-file_allCalphas.pdb", where you change the occupancy of the atoms that you want to drive toward the other conformation to 1 and keep the occupancy of the others 0. This can be done easily with VMD (or with any other method that you feel comfortable with). A short production or equilibration before TMD would be useful.
Good luck,
Mustafa
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