[AMBER] Problem in designing MD simulation based on Experimental data

From: Bharat Manna <bharatmanna.gmail.com>
Date: Fri, 16 Nov 2018 07:53:12 -0800

Dear All,

I am working with some enzyme activity experiments in different solvents
and temperatures. The enzyme seems to get inactivated (structural breakdown
based on expt. data) at a temperature of around 80 °C. So, I designed an MD
simulation (same enzyme class PDB structure was taken) with proper solvents
at 353K (80 °C) using AMBER 18. However, I didn't find any significant
structural changes in the enzyme during the simulation (150ns). Is it right
to increase the temperature (e.g. 400K to 500K)? If yes, will the
simulation results be applicable to support the experimental findings
(performed at a significantly lower temperature)?

Please help.

Thank you.
B Manna
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Received on Fri Nov 16 2018 - 00:00:02 PST
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