AMBER Archive (2009)

Subject: [AMBER] Free Energy Decomposition Problem

From: ozlem ulucan (
Date: Mon Mar 09 2009 - 08:55:45 CDT

Dear Amber Users,

I am trying to compute free energy contribution of each residue using MM_GBSA. My system includes some non-standart residues such as mono-, di-, tri-methylated lysine and FE, ZN ions. I have already inserted the parameters for ZN and FE ions into mdread file as suggested in previous posts.( There is no problem with MM-GBSA/MM-PBSA calculations.) When I try to compute free energy decomposition I always face the same problem:

 'Missing values for MM BGAS'.

 I tried to find out which amber file includes this error message, but unfortunately I could not find. Any suggestions and comments will be highly appreciated.

Thanks in advance.

Koc University, TURKEY


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