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About Acid and Basic Conditions
#1271 04/18/04 01:41 PM
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freesky Offline OP
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Dear all
I want to know how to run a simulation in the acid or alkaline solution? Any suggestions?

Thank you!




---- State Key Lab of Solid State Microstructure Nanjing University P.R.C
Re: About Acid and Basic Conditions
freesky #1272 04/21/04 12:23 PM
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Set the protonation state of titratable groups to whatever is appropriate for the pH you have in mind. In the pH range 2-12 there is little if any possibility to have OH- or H3O+ explicitly present; pH 3 corresponds to one H3O+ for 55000 water molecules ...


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: About Acid and Basic Conditions
lennart #1273 04/22/04 12:57 PM
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freesky Offline OP
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Could you please explain the correlations between the protonation state of titratable groups and the PH values detailedly?
Thank you very much!


---- State Key Lab of Solid State Microstructure Nanjing University P.R.C
Re: About Acid and Basic Conditions
freesky #1274 04/22/04 01:14 PM
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You need to make a scientific decision about each titratable group based on the pH of the solution and the ACTUAL pKa of the group (in a protein this may differ substantially from the standard values for free amino acids found in biochemistry text books).
An understanding of some fundamental concepts in chemistry, such as pH, is a necessary foundation before undertaking simulations of biochemical systems, and you should consider taking a biochemistry course or read a good biochemistry text book before you proceed too far with your simulations.



Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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