Re: [AMBER] qm-mmgbsa error

From: Jason Swails <>
Date: Tue, 21 Jul 2015 12:23:20 -0400

On Tue, Jul 21, 2015 at 12:55 AM, Ayesha Fatima <>

> Dear All,
> I have run 2ns qm/mm on a stabilised ligand-protein complex using AMBER12.

I want to calculate the free binding energy. First I used the
> using the script by Holger Gohlke. I modified the &GB section to include
> the qm parameters. The output returned positive values for GBTOT which are
> rather high.
> Then I tried to use the method and created the file as
> indicated on the mailing list. The mdins files were created and as
> mentioned on the mailing list to remove the "dec_verbose" and rerun the
> mmpbsa. I did that however the error of CalcError: sander failed with
> prmtop ../! is coming.
> Can someone guide me to set up?

​Do you get the same issue when you run with AmberTools 15? Amber 12 is
rather old at this point (released over 3 years ago), and there have been
numerous fixes and improvements to since then.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Tue Jul 21 2015 - 09:30:03 PDT
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