Re: removing waters from big dcd files

From: Jerome Henin (
Date: Mon Jul 16 2007 - 12:17:20 CDT

Hi Rebeca,

On 7/16/07, <> wrote:
> 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,

I would have expected this to work. A problem you may have is the
difference between PDB files and VMD for atom numbering - VMD uses
0-based indices while PDB indices are 1-based (that is what catdcd
expects). If you use VMD to determine the indices, add one to get PDB


> 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
> donīt 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

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