On 7 August 2013 17:26, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
Hi Dan,
Many thanks for replying.
>
> On Wed, Aug 7, 2013 at 8:05 AM, Massimiliano Porrini
> <m.porrini.iecb.u-bordeaux.fr> wrote:
> > mask "(:1-27>:25.0)&:COP" maskout filename.dat maskpdb filename.pdb
>
> The distance-based mask syntax can be a little tricky to parse
> through. Your mask here literally means "Select an entire residue if
> any part of it (i.e. any atom in that residue) is farther than 25.0
> Ang. away from any atom in residues 1-27", *not* the center of mass of
> residues 1-27. So just be aware that when you have multiple atoms in
> the first part of your distance-based mask it's not really a sphere
> you're using as your criterion; in this case it's actually somewhat
> dependent upon the overall configuration of the atoms in residues
> 1-27.
>
Aw! OK then.
Given that it is distance-based syntax, I just assumed that the same rules
as in "distance" command apply here, i.e. if there are more than one single
atom
in the mask, cpptraj will consider their COM.
I raise a question then: is there any way to consider the COM of the mask ?
> > and I obtain that, *in each* of the 10 frames all the 54 counterions are
> > beyond 25.0 Angstroms,
>
> It does seem strange that every counterion is beyond 25.0 Ang. What
> exactly is the COP residue (is it a single atom?).
>
Indeed, COP is a single atom, specifically the chloride anion and I used
the same name
for both the atom and the residue to which it belongs to.
>
> > mask "(:1-27<:25.0)&:COP" maskout filename.dat maskpdb filename.pdb
>
> Just to clarify, this mask literally means "Select an entire residue
> if any part of it is within 25.0 Ang. of any atom in residues 1-27".
>
> > I obtain the following numbers of counterion per each of the 10 frames
> >
> > 49, 49, 48, 43, 48, 46, 48, 50, 52 and 45
> >
> >
> > If the results of [1] are correct I should obtain all 0 in [2].
> >
> > Conversely, if the results of [2] are correct, I should have obtained
> > the following results in [1] (i.e. the complementary numbers to 54):
> >
> > 5, 5, 6, 11, 6, 8, 6, 4, 2 and 9
>
> I think that when you select based on residue (i.e. <: vs <.) this is
> only true if COP is a single atom. Otherwise there can be some overlap
> for residues on the border of your distance criterion.
>
In fact your assumption is correct: COP is a single particle.
>
> If you would like, send me off-list your topology and a single frame
> for your system and I'll try to figure out what exactly is going on.
>
I am going to send you the files.
Thanks again for your help!
Max
> -Dan
>
> --
> -------------------------
> 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) 585-9119 (Fax)
>
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--
Dr Massimiliano Porrini
Institut Européen de Chimie et Biologie (IECB)
CNRS UMR 5248 Chimie et Biologie des Membranes et des Nano-objets (CBMN)
2, rue Robert Escarpit
33607 Pessac Cedex
FRANCE
Tel : 33 (0)5 40 00 30 31
Fax : 33 (0)5 40 00 22 00
http://www.iecb.u-bordeaux.fr/
Emails: m.porrini.iecb.u-bordeaux.fr
M.Porrini.ed.ac.uk
maxp.iesl.forth.gr
mozz76.gmail.com
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Received on Wed Aug 07 2013 - 10:00:03 PDT
