From: regafan_at_usc.es
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 $i.pdb"
}
exit
but anyway, the first and last structure of the trajectory
generated,myprotein_prot.dcd, do not correspond with the first and
last structure of the corresponding coor files. I am not an expert on
vmd, do you see something wrong in this script which can be the cause
it doesnt work properly?
Rebeca Garcia Fandiņo
Parc Cientific de Barcelona
regafan_at_usc.es
Estase citando Dong Luo <us917_at_yahoo.com>:
> You can write a script by yourself to fufill the job.
> Check the VMD user guide for the usage of "animate".
> It can be used to read in just part of a big DCD file.
> Make a "atomselect" excluding water molecules, you can
> use "$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.
>
> --- regafan_at_usc.es 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
>> regafan_at_usc.es
>>
>>
>
>
>
>
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