Re: [AMBER] Distance tolerance for identifying common atoms in thermodynamics integration

From: David A Case <>
Date: Fri, 26 Mar 2021 16:40:19 -0400

On Fri, Mar 26, 2021, zz sheng wrote:
>I am preparing the softcore mask for TI simulation. Two copies of the
>receptor was included in one file with one amino acid mutation for topology
>file preparation by tleap. It turns out that tleap alters slightly the
>coordinates of the backbone atoms of the mutated residues which should
>assumably be identical between the two receptor copies. So now Amber can
>not identify common backbone atoms because of the coordinate changes. I
>wonder if there are parameters can be set to adjust the distance tolerance
>for identification of common atoms in Amber. Or, to disable tleap to change
>the coordinates?

This is odd: it would be nice if you could create a small example showing
the problem. What do you mean by the term "slightly"?

Also, try adding the following command at the beginning of your
tleap script, to see if it helps:

    set default nocenter on

But this is a guess: if the WT and mutated atoms have identical coordinates
in the input structure, that relationship should not be changed by tleap.


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Received on Fri Mar 26 2021 - 14:00:03 PDT
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