Dear Sir
Wish you are fine!
Concerning the system setup of Amber tutorial B3 for the purpose of All
Atom Structure Prediction and Folding Simulations of a Stable Protein.
http://ambermd.org/tutorials/basic/tutorial3/
Why did not he check the charge of the system and add suitable counter ions
to neutralize it before the simulation? I checked the supported
TC5b_linear.pdb
<
http://ambermd.org/tutorials/basic/tutorial3/files/TC5b_linear.pdb> with
XLeap and I found that it has a total charge of +1. I am trying to run
similar simulations on a system that has a total charge of +6. Do you think
that neutralizing this system or any other system undergoing this type
of folding
simulations may affect the results significantly?
Regards
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Received on Thu Apr 13 2017 - 16:00:03 PDT
