Re: removing waters from big dcd files

From: Dong Luo (
Date: Mon Jul 16 2007 - 14:40:55 CDT

You can write a script by yourself to fufill the job.
Check the VMD user guide for the usage of "animate".
It can be used to read in just part of a big DCD file.
Make a "atomselect" excluding water molecules, you can
use "$yourselection writedcd dcdpartname" to output
this part and "animate delete all" to clear it. Repeat
for all parts. Finally use "animate" to read all
output dcd files one by one to combine them into the
new psf structure.

--- 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, 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

Pinpoint customers who are looking for what you sell.

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:44:58 CST