From: Nicholas M Glykos (
Date: Fri Apr 06 2012 - 02:37:50 CDT

> Sorry for my unclear email. My dcd file is very big 30GB and if I try to
> open, my computer freezes. That is why I am searching some tcl script to
> strip water and ions. Could you please help me.

Or, if you want to keep it simple, you can install carma and then say
(from the unix shell) :

carma -v -w -fit -atmid ALLID -segid A -segid B -segid C my.dcd my.psf

where A,B,C are the SEGIDs you want to keep. As a bonus your new dcd file
(carma.fitted.dcd) will also have rotations/translations removed using
Kabsch's algorithm.

            Nicholas M. Glykos, Department of Molecular Biology
     and Genetics, Democritus University of Thrace, University Campus,
  Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
    Ext.77620, Tel (lab) +302551030615,

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