Re: [AMBER] Centre of Mass or geometry issue

From: Jason Swails <>
Date: Tue, 9 Jun 2015 07:36:59 -0400

On Tue, Jun 9, 2015 at 5:14 AM, Juan Eiros Zamora <> wrote:

> Hi,
> If you add the @CA it means you're only selecting the alpha carbons of
> your residues, and you have to write it both times and the end of your
> residue selection. So it should be like this:
> distance R1-R2.CA R3.CA out xyz.dat

​Almost. The mask syntax is :R.A, where R is a residue number or name and
A is an atom number or name. So you are missing the leading ":" on both R1
and R3. Also, as written, R1-R2 specifies a residue *range*, meaning that
it will select all residues between numbers R1 and R2 (inclusive). To
select *just* residues R1 and R2, the command would look something like

distance :R1,R2[.CA] :R3[@CA] out xyz.dat

I put the .CA in [] to signify that it's optional (omit the []'s if you
want to specify the atom names). As you mentioned, specifying that will
restrict the two selections to the CA atoms of those residues (and if this
is the case, since all CA atoms have the same mass, COM is the same as COG).

> And that will calculate the distance between the center of mass of R1.CA
> and R2.CA to R3.CA. If you want to calculate the center of mass for all
> the atoms in the residues, drop the .CA



Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Tue Jun 09 2015 - 05:00:02 PDT
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