PDB file creation

From: matthew reeves (mreeves94_at_gmail.com)
Date: Tue Feb 07 2017 - 17:52:08 CST


I’m preparing to run a namd simulation on a growth hormone bound to a receptor to see how the energy evolves with time. I am able to isolate each of the two chains in the molecule but I need them at a set distance away from each other before starting the simulation.

 I seem to be having trouble creating the necessary PDB file for the whole system after I have set the two chains at the desired distance apart (after translation, rotation etc.). The ‘writepdb’ command doesn’t seem to work in this scenario but rather produces a PDB file that returns the two chains to their original position.

Is there any way that a separate PDB file can be created for the final positions of the chains? Any advice would be greatly appreciated.


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