Re: [AMBER] deltaG binding obtained from AmberTools 12 and 13 are different

From: Xioling Chuang <>
Date: Wed, 4 Sep 2013 04:06:50 +0200

Dear Jason,
Thank you very much again for your message.
I have tried to calculate entropy using quasi-harmonic approximation with The input is

   startframe=1, endframe=1,
   interval=1, keep_files=0,
  igb=2, saltcon=0.0,

I got three lines of warning message as
"Warning in analyzeMatrix: bad eigenvalue 0 0.00"
and the entropy result is 0.00 for all Tran., Rot. and Vib.

Please suggest.

Best Regards,

> I don't know. They use their own set of programs/scripts to handle it. I
> would suggest reading their papers and/or visiting their website for hints.
> This is not implemented directly by any Amber programs, so it may be that
> nobody that responds on this list knows.
> Good luck,
> Jason

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Received on Tue Sep 03 2013 - 19:30:02 PDT
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