From: bishop_at_latech.edu
Date: Thu Jul 11 2013 - 13:01:33 CDT
HEre's what I do...to yank dna from all my dcds for analysis on the fly.
you can redirect "tmp.pdb" to fastest HD/SSD/ram whatever on your system
to speed things up .
(i've edited this a bit some might bemissing a bracket or so)
### usage: vmd -psf some.psf -e thisfile.vmd -args 1.dcd 2.dcd 3.dcd
#### or vmd -parm7 some.parm -e thisfile.vmd -args if you use amber
set nucsel [atomselect top nucleic]
foreach dyn $argv {
mol addfile $dyn type {dcd} first 0 step 1 waitfor all 0
set numframes [molinfo top get numframes]
puts "loaded $numframes for $dyn "
for {set i 0} {$i < $numframes} {incr i } {
puts " ***************** "
puts " frame $i of $numframes $dyn: parcnt $parcnt"
puts " "
$nucsel frame $i
$nucsel writepdb tmp.pdb
## analyze "tmp.pdb" on the fly with whatever you want here and cleanup
}
animate delete all
}
quit
Quoting Aron Broom <broomsday_at_gmail.com>:
> you should look through the VMD manual's text commands section. You could
> write a script that you run at load time which just does that saving for
> you. If you only need to do this infrequently, you could just use the VMD
> GUI and save as a pdb over the frame range you are interested in.
>
>
> On Thu, Jul 11, 2013 at 10:43 AM, Gabriel Jara <gabriel.fcq.unc.ar_at_gmail.com
>> wrote:
>
>> HI,
>>
>> do you try with catdcd?
>>
>> Gaby
>>
>>
>> On Thu, Jul 11, 2013 at 9:40 AM, oguz gurbulak
>> <gurbulakoguz_at_yahoo.com>wrote:
>>
>>> Dear NAMD users,
>>>
>>> I want to generate pdb files which include the same number of records
>>> from a dcd file for data analysis. For example my dcd file has 4000
>>> records. And I want to produce four pdb files contain 1000 records (1.pdb,
>>> 2.pdb 3.pdb and 4.pdb). How can I divide a dcd file into the pdb files
>>> easily and quickly ?
>>>
>>> Thanks for your help.
>>>
>>
>>
>>
>> --
>> Dr. Gabriel E. Jara
>> Laboratorio de Modelado Molecular
>> INQUIMAE - Instituto de Química-Física de Materiales, Ambiente y Energía
>> DQIAyQF - Departamento de Inorgánica, Analítica y Química-Física
>> FCEyN - Facultad de Ciencias Exactas y Naturales
>> Universidad de Buenos Aires
>> Intendente Güiraldes 2160 - Hall 2, 1er piso.
>> Ciudad Universitaria - C1428EGA
>> Buenos Aires - Argentina
>> Tel: +54 11 4576 3378 /79 /80, int. 123
>> ------
>>
>>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
>
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