Dear Amber users and developers,
I am trying to use the valuable mask command in cpptraj of AT13.
My system is made up of one solute (27 residues, numbered from 1 to 27)
and 54 counterions (named COP).
My purpose is to count, per each frame, the number of counterions whose
distance from
the centre of mass of the solute is greater than 25.0 Angstroms.
[1] After reading 10 frames of one DCD trajectory file, I attempted to use
mask command to
accomplish the above purpose:
trajin dyn.dcd 1 1000 100
mask "(:1-27>:25.0)&:COP" maskout filename.dat maskpdb filename.pdb
and I obtain that, *in each* of the 10 frames all the 54 counterions are
beyond 25.0 Angstroms,
which is clearly not possible (the DCD file I am using is related 10 ns
after 40 ns of dynamics).
[2] On the other hand, if I count the number of counterions which are
supposed to be within 25.0 Angstroms from the centre of mass of my solute:
trajin dyn.dcd 1 1000 100
mask "(:1-27<:25.0)&:COP" maskout filename.dat maskpdb filename.pdb
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
Does anybody have any suggestion about this issue?
Am I using the correct mask syntax in mask command?
Thanks a lot in advance,
Best,
--
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 - 07:30:02 PDT
