removing waters from big dcd files

From: regafan_at_usc.es
Date: Mon Jul 16 2007 - 11:08:57 CDT

Hello,

I would like to remove the waters from from a dcd file obtained with
NAMD/Charmm, and the problem is that the size of the file is 2.9 G
(with waters). I have tried to use ptraj to obtain the "dry
trajectory", and I got a quite strange trajectory, with a first and a
last step different from the structure of the corresponding first and
last .coor files. I have also tried to use catdcd, choosing the
indexes of only the protein, but when I visualize the resulting
trajectory, loading first the psf of the protein without the waters, I
cannot visualize the tertiary sctructure, it is only a ribbon what I
can see.
I have seen that there is also a script for big files, "bigdcd", but I
don´t know how to use it to eliminate the waters, and if this is
posible.
Could anyone help me with the treatment of this big dcd files?
Thanks a lot!

Rebeca Garcia Fandiņo
Parc Cientific de Barcelona
regafan_at_usc.es

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