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
looking for.
The residue numbering in the initial pdb loaded into leap was ignored. The
first residue in the file was labeled 1...

Thanks again.

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
> double
> check to remove the space or use quotation marks, like
>
> atoms ":308-317, 321-331_at_CA"
>
>
> Thanks,
>
> Jianyin
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