AMBER Archive (2009)
Subject: Re: [AMBER] ptraj mask selection
From: Patrick Gedeon (patgpgh_at_gmail.com)
Date: Mon Jul 13 2009 - 14:58:18 CDT
Thank you for the info. The atoms command in rdparm was just what I was
The residue numbering in the initial pdb loaded into leap was ignored. The
first residue in the file was labeled 1...
On Mon, Jul 13, 2009 at 3:02 PM, Jianyin Shao <jyshao2004_at_gmail.com> wrote:
> On Mon, Jul 13, 2009 at 12:10 PM, case <case_at_biomaps.rutgers.edu> wrote:
> > On Mon, Jul 13, 2009, Jianyin Shao wrote:
> > > 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
> > ^^^^^^^^^^^^^^^^^^^^^
> > I think you should/must avoid spaces in atom masks.
> > ....dac
> > Sorry, that's my bad. I just copied the text and pasted it. I should
> check to remove the space or use quotation marks, like
> atoms ":308-317, 321-331_at_CA"
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