AMBER Archive (2009)

Subject: [AMBER] ptraj mask selection

From: Patrick Gedeon (
Date: Sun Jul 12 2009 - 22:45:56 CDT

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

"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

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