Thanks a ton.
On Sun, Dec 8, 2013 at 9:59 PM, case <case.biomaps.rutgers.edu> wrote:
> On Sun, Dec 08, 2013, sunita gupta wrote:
>
> > I have a protein-lignad complex (231 residues protein and 232nd residue
> as
> > ligand). While setting up MD for this complex I want to fix the protein,
> > and if I am selecting ':1-231' as restrainmask, it is selecting the
> ligand
> > as well.
>
> NAB atom expressions are different than those in the rest of Amber: they
> have three sections (chain (aka strand, aka molecule), residue, atom), and
> the residue numbers start over at 1 for each new chain.
>
> Hence, you atom expression selects residues numbered 1-231 in each chain:
> this
> will include the ligand (which is presumably the first residue in the
> second
> chain.) What you probably want is "1::" (for the entire first molecule).
>
> ...good luck...dac
>
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--
--
SUNITA GUPTA
Senior Research Fellow
Bioinformatics Centre
Jawaharlal Nehru University
New Delhi- 110067
Email- sunita.bio.gmail.com
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Received on Sun Dec 08 2013 - 21:30:03 PST
