Re: [AMBER] Unable to run decomposition analysis using of amber12

From: Jason Swails <>
Date: Mon, 9 Sep 2013 15:49:42 -0400

On Mon, Sep 9, 2013 at 3:27 PM, Manikanthan Bhavaraju <> wrote:

> Jason,
> Thanks for the reply. %FLAG ATOMIC_NUMBER" does exists in the
> complex.prmtop file. The complex, receptor, and ligand prmtop files were
> made using tleap of Amber12, but not Ambertools 12 or 13.

No, Amber 12 is _just_ sander and pmemd. [1] AmberTools contains all of the
prep and analysis programs (e.g., tleap, cpptraj, ptraj,, etc.).
 You can use the command "$AMBERHOME/update_amber --version" to get the
full version of Amber/AmberTools that you are using.

> The C0 is for a
> carbon atom, it is for Ca+2 ion. Is the labelling for Ca+2 in ff99SB is C0
> or CO?

Then you will have to add a radius for calcium where I pointed you to in my
last email. Note, ions are not well-studied with implicit solvent models
like GB, so you should be wary of your results.

Good luck,

[1] It also includes addles and, but sander and pmemd are the
more commonly known programs from Amber.

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Mon Sep 09 2013 - 13:00:02 PDT
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