AMBER Archive (2004)

Subject: AMBER: pka calculation

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dear amber users,
  I am performing a MD simulation by using amber.A fatty acid(oleic acid) binds to the protein I'm working on.Now I wanna to determine the charge state of the fatty acid.some literatures recommend a shift-of-pka calculation of the carboxylate group of the fatty acid by using DELPHI.But I don't know how to perform such a calculation in detail.
Can anyone tell me the procedure of calculation? the more detailed ,the better.
Thank you in advance.

best regards
¡¡¡¡¡¡¡¡¡¡¡¡2004-02-23

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• Next message: David A. Case: "Re: AMBER: How to add ACE and NME groups?"
• Previous message: uddhavesh bhaskar sonavane: "AMBER: protein - fractional native contacts"
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