Re: removing waters from big dcd files

Date: Mon Jul 16 2007 - 15:01:12 CDT

Thanks a lot for your help. I get the indexes of the protein using

seq ?f ?%04g? ?s " " 2573

so I get a file of the type

0001 0002 0003 0004 (...)2573

I have also tried with a index file of the type

1 2 3 (...) 2573

But any of them gives me an adequate visualization of the dcd file
generated with catdcd using vmd. Do you think is it problem of the
index numbers?

  Rebeca Garcia Fandiņo
  Parc Cientific de Barcelona

Estase citando Jerome Henin <>:

> 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
> indices.
> Jerome
>> 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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