AMBER Archive (2009)

Subject: Re: [AMBER] ptraj mask selection

From: Jianyin Shao (
Date: Mon Jul 13 2009 - 12:57:23 CDT

Hi Patrick,

I think the numbering of residues could be different from that of your
original pdb file. You can use rdparm, a sister program of ptraj, to check
the mask selection.

rdparm your_prmtop

atoms :308-317, 321-331_at_CA

That should print out the atoms specified by the mask.



On Sun, Jul 12, 2009 at 9:45 PM, Patrick Gedeon <> wrote:

> Hello,
> I am using ptraj to preform some operations only for a subset of residues.
> I
> am selecting the residues and I see the following in my output file for
> example:
> "Mask [:308-317, 321-331_at_CA] represents 21 atoms"
> How can I see exactly which residues this corresponds to (is it the
> numbering in the resid column of the pdb loaded into leap to create the
> prmtop or numbering based on residues loading into leap starting at 1,
> etc)?
> I ask because my pdb file loaded into leap had some N-terminal residues
> missing. (So the first residue in the pdb file loaded into leap corresponds
> to 5th residue of protein, numbered 5 in the pdb)...knowing this, what is
> the numbering scheme I should use to select residues in ptraj
> Thanks.
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