On 7 August 2013 19:59, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> I received your files and I know what is going on now. Again, the
> given "without" mask:
>
> "(:1-27>:25.0)&:COP"
>
> means "Select an entire residue if any part of it is farther than 25.0
> Ang. away from any atom in residues 1-27 AND it's residue name is
> COP". All COPs are selected because as it turns out for every COP atom
> there is always an atom in residues 1-27 that is farther away than
> 25.0 Ang (the entirety of residues 1-27 is roughly 32-45 Ang. across).
> So to put it another way, even if you have a COP ion right next to
> residues 1-27, there is an atom on the opposite side of residues 1-27
> that is farther than 25 Ang away.
>
> Therefore, for your purposes its probably better to use the "within"
> mask and then subtract from 54 as you were doing. Based on the frame
> you gave me this seems to give the results you want. Let me know if
> this seems unclear.
>
It is crystal clear ;-)
And actually it supports what I was going to do: to utilise
the "within" mask and then subtract the results from 54.
One question: is there any way to define the distance
from the centre of mass (or even the geometric centre) of my solute?
I am asking this because the way I make mask command work now will take
into account
more counterions than those that would be included in a sphere of radius 25
Angs
and centred in the centre of mass (or geometric centre) of the solute.
Thanks a lot for your precious help.
Best,
>
> -Dan
>
> On Wed, Aug 7, 2013 at 10:30 AM, Massimiliano Porrini
> <m.porrini.iecb.u-bordeaux.fr> wrote:
> > 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)
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> 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)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Aug 07 2013 - 13:30:03 PDT
