[AMBER] TI calculation problem in pmemd

From: cuiyinglukitty <cuiyinglukitty.gmail.com>
Date: Mon, 19 Dec 2016 14:34:12 +0800

Dear Amber users,
I am trying to calculate the Thermodynamic Integration using soft core potentia
ls in tutorial A9. The dG value in my calculation for A99V protein is -10.19 k
cal/mol. However, the tutorial suggests that the alanine mutant is favoured ov
er the valine mutant by about 10 kcal/mol. Should I also calculate the dG value
 for the complex, and then use the value = dGcom - dGprotein? If I want to calc
ulate the sidechain mutations in a protein without any ligands, can I only use
the dG value for the protein without performing any complex calculations?

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Received on Sun Dec 18 2016 - 23:00:02 PST
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