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.
-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
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> 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)
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Received on Wed Aug 07 2013 - 11:30:02 PDT
