AMBER Archive (2009)

Subject: [AMBER] how to add a new atomtype for MM/GB/SA decomposition analysis

From: TaoPaul (
Date: Mon Aug 24 2009 - 09:03:51 CDT

Dear all,

I am trying to do a free energy decomposition analysis and I encountered a problem
that the parameters for fluorins (atoms in the ligand) are absent, shown as following:

=>> Calculating energy / entropy contributions
    Calc contrib for ../snapshot_com.crd.1
        Calc MM/GB/SAS
 bad atom type: f
        /share/apps/amber9/exe/sander -O -i -o sander_com.1.out -c ../snapshot_com.crd.1 -p ../ not successful

What I want to ask is what parameters are needed and if I got how and where should I add them to compute successfully?

Jin Tao
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