Hi,
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.
> 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?).
> 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.
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.
-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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Received on Wed Aug 07 2013 - 08:30:02 PDT
