Re: removing waters from big dcd files

Date: Mon Jul 16 2007 - 15:09:01 CDT

Thanks for your suggestion,

I have tried with this script:

mol load psf solvated.psf dcd md0001.dcd
set nf [molinfo top get numframes]

for {set i 0 } {$i < $nf } {incr i 100 } {
   set sel [atomselect top protein frame $i]
   $sel writepdb $i.pdb

mol load psf dry_prot.psf

for {set i 0 } {$i < $nf } {incr i 100 } {
   animate read pdb $i.pdb }

animate write dcd {myprotein_prot.dcd} waitfor all top

for {set i 0 } {$i < $nf } {incr i 100 } {
puts "Removing file $i.pdb"


but anyway, the first and last structure of the trajectory
generated,myprotein_prot.dcd, do not correspond with the first and
last structure of the corresponding coor files. I am not an expert on
vmd, do you see something wrong in this script which can be the cause
it doesnt work properly?

  Rebeca Garcia Fandiņo
  Parc Cientific de Barcelona

Estase citando Dong Luo <>:

> 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
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