Hi, I am trying to align two protein complexes - structure before the start of simulation and the structure isolated at 1ns simulation. despite having the same number of atoms, I have been getting the error that the selections must have the same number of atoms. can someone suggest an idea?
Dear Dinesh,
I use to have similar errors when I started learning Molecular Dynamics.
The error is due to some glitch from the .tcl file that is supposed to execute that request (the atom labeling after preparation of the apo is now different) because it couldn't find the right parameter file.
The perfect solution is this, it might be tasking for the current job (seeing that you have put in so much effort to reach this stage) but you have to prepare your protein or complexes using the charmmGUI "solution builder" option.
It will further help you in future research.
https://www.youtube.com/watch?v=1M16HBY7_aU
I hope this helps a bit.
Best wishes.
thank you Salau Samuel Shina .. will check out the tutorial!
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