Hello armlet,
It will be strip :1-500 {as : denotes residues and . denotes atoms } for e.g. :1-500.CA,C,N will backbone atoms of residues 1 to 500 and :1-500 will mean all atoms of residues 1-500
Best,
Nitin
-----Original Message-----
From: Marlet Martinez [mailto:marletm8.gmail.com]
Sent: Tuesday, April 22, 2014 11:43 PM
To: AMBER Mailing List
Subject: Re: [AMBER] strip some atoms to compute RMSD
Dear all,
Thanks for your kind response
Actually what I was trying to do was to "mask" or "strip" some atoms that correspond to several residues of one of the chains of my protein. So I
was wondering If I should do: strip .1-500 in order to mask all the
atoms that belong for the chain that has 500 residues (1-500) is that correct?
I guess for RMSD, RMSF I should use the same instruction if I want to mask those atoms , right?
Thank you so much for your suggestions
2014-04-22 16:10 GMT+02:00 Daniel Roe <daniel.r.roe.gmail.com>:
> Hi,
>
> On Tue, Apr 22, 2014 at 6:12 AM, Asaminew Haile <ashaethio.gmail.com>
> wrote:
> >
> > On Apr 22, 2014, at 7:56 AM, Marlet Martinez <marletm8.gmail.com> wrote:
> >
> >> Dear Amber users,
> >>
> >> I am training to make some structural analysis in just of the two
> chains
> >> of my protein, since their numbering is exactly the same e.g 1-20
> >> and
> the
> >> both are named as chain "C"
> >>
> >> So I was wondering if there is a way in amber to strip atoms instead of
> >> residues like when executing strip command e.g: strip: 1-20
>
> The atom selection syntax character is '.', so if you want all atoms
> named 'OP1' for example you would use the mask '.OP1', etc.
>
> > example
> > strip 1-20.H*
>
> I think you meant ':1-20.H*' (without the residue ':' operator this is
> an invalid mask). See section 28.2.3 of the Amber14 manual for a more
> detailed description of mask selection syntax, including several
> examples.
>
> Hope this helps,
>
> -Dan
>
> > will strip all Hydrogen
> >
> >> (this only
> >> works to "mask" residues but not atoms" in order to perform RMSD
> >> calculation.
> >>
> >> Thanks in advance,
> >>
> >> Best regards
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> >
> >
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>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
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Received on Tue Apr 22 2014 - 09:00:02 PDT
