AMBER Archive (2009)

Subject: [AMBER] PBSA for gp41 binding free energy

From: shuqing wang (
Date: Fri Sep 11 2009 - 01:42:59 CDT

Dear Amber users:
      I am a new user of Amber, now try to compute the binding free energy of the peptides system which are extracted from the GP41, for example the pdb code(1env). The receptor is the core three N-terminal called 3N,the peptide drug is T20, a HIV-1 inhibitor.(see attachment)
     I want to know weather the amber program take the peptides as one ball protein?
    which module of Amber can do this computation?
    My result of PBSA in attachment file, and the PBSUR too big can not as the experiment result. who know the reason.
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  • X-unknown/x-pdb attachment: 3N.pdb

  • X-unknown/x-pdb attachment: SFT.pdb

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