Dear all,
I want to mimic the process of protein synthesis. How can I turn on/off the residues in the protein?
Thank you and best regards,
Quyen
@Bojidarka no matter what program package, do you know how to do it, please help me! Thank you so much
Quyen V. Vu Your question is unclear. In terms of simulation, if you have a crystal structure (.gro, .pdb, .xyz, etc., format) you can mutate one of the residues to another one by means of pymol. It is impossible just remove one of the resides from the whole structure. It leads to fragmentation of the protein. If you prefer to build up protein with specific sequence you can use Avogadro or Swiss.
Jamoliddin Razzokov I am sorry that my question is not clear.
By using turn of residues in protein, I mean that:
e.g my protein have 10 residues in pdb file.
the topology will have the information about the protein structure but to mimic the synthesizing process,
-at t=0, the program will only calculate the interaction of residue 1 (although the structure is still 10 residues )
-at t=1ns (for example), the program will only calculate the interaction of residue 1 and residue 2 (although the structure is still 10 residues )
...
...
-at t=10ns (for example), the program will only calculate the interaction of full protein.
Is it clear now?
Thank you
Quyen
Dear Bojidarka B. Ivanova , Jamoliddin Razzokov
I attach here the quick draw picture of what I am saying, please take a look: https://www.dropbox.com/s/eycsm3qsywhgxjv/model.pdf?dl=0, thank you and best regards,
Quyen
I'm not sure what you hope to obtain with such a calculation. The timescale of protein synthesis is orders of magnitude longer than what you can conduct with any MD simulation. You could certainly conduct N simulations with an additional residue tacked onto the end of your protein for each new simulation. Again, this will not lead to anything that you could hope to compare with experiment.
If your intent is to turn on each of the residues during the course of a single simulation, this does not correspond to any physiological process. Residues do not materialize from thin air; they diffuse into the active site. Perhaps you want to create some sort of instructional animation?
If you still want to proceed, you could just define new residues where all of the forcefield parameters for your new residues are zero. Then, after some length of simulation, you could reload the forcefield file with the parameters for the first residue redefined to their nominal values. Then run another simulation with the first two residues repaired, etc. When you've finished all N of them, you can stitch together the trajectory files for whatever analysis you intend. This will require a lot of work on your part for no apparent gain but perhaps you have greater insights into what you want to accomplish than what you have conveyed thus far. The bottom line, though, is that no MD package, to my knowledge, will permit you to do what you want with existing commands.
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