From: Jason Swails <>
Date: Wed, 11 Jun 2014 08:35:07 -0400

On Wed, 2014-06-11 at 12:31 +0100, John Smith wrote:
> Hi AMBER users,
> Could you please help me with the command for running QM based binding
> energy calculation. I have a prmtop file for the solavted complex, a prmtop
> file for the complex, a prmtop file for the protein on its own and the
> ligand on its own. The iput file I am using is:
> &general
> startframe=1, endframe=200, interval=5,
> ifqnt=1, qmcharge=0, qm_residues='123, 432'
> qm_theory='PM3', qmcharge_lig=1, qmcharge_rec=-1
> /
> &gb
> igb=5, saltcon=0.100,
> /
> I know that it requires a *sander *functionality but I could not implement
> this into the command. will automatically use sander when it needs to (such as when
you are using QM/MM-GBSA). You don't have to _do_ anything else special
in your input file.

In the past, sander was released as part of Amber (not AmberTools), and
so you needed a paid license to run QM/MM-GBSA calculations (or anything
else requiring sander) -- that is why the distinction was made. This is
no longer the case.

> I am also trying to run nmode binding energy calculation using the same
> prmtop files mentioned above and the following inout file:
> &general
> endframe=200, keep_files=2,
> /
> &nmode
> nmstartframe=1, nmendframe=200,
> nminterval=5, nmode_igb=1, nmode_istrng=0.1,
> /
> The calculation takes hours and then stops recording an error in the prmtop
> file for the non-solvated complex. I have used these exact prmtop file to
> run ordinary GB and PB free energy calculations and they are working fine
> for me.

Try Googling the exact error message you get. My guess is that someone
else has seen this problem before and there will be old threads that
tell you the problem.

We cannot help when all we know is "something did not work". We need
output, error messages, and input (copy-and-paste, do not paraphrase).


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Wed Jun 11 2014 - 06:00:04 PDT
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