Dear Sir/Madam,
I would like to determine the potential energy changes for drug binding the receptor and for the drug remove from the receptor. In practice, the PMF of binding should be lower than that of removing, otherwise no drug-receptor complex could be formed.
I tried to use umbrella sampling method to determine the PMF as a function of distance between the drug and receptor. As the drug removal and drug binding process use the same path (defined as the distance between the drug and the receptor). I can only see PMF for binding and removal are the same.
I noted that I can define steered MD by start and end point. Should I expect to see the PMF obtained by binding and removal of drugs are different using these two different SMD restraints?
(1)
# Change distance between atoms 485 and 134 from 15 A to 20 A
&rst iat=485,134, r2=15., rk2 = 5000., r2a=20. /
(2)
# Change distance between atoms 485 and 134 from 20 A to 15 A
&rst iat=485,134, r2=20., rk2 = 5000., r2a=15. /
Please kindly help.
Cat
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Received on Wed May 19 2010 - 23:30:04 PDT
