VMD-L Mailing List

From: jouko_at_berkeley.edu
Date: Tue Jan 06 2009 - 22:32:51 CST

Thanks. I got it to work.

> Dcd files can be very easily manipulated with catdcd tool. For example,
> you
> can extract every 100th frame, you can select first and last frames and
> thus split the original trajectory into several sub-trajectories.
>
> http://www.ks.uiuc.edu/Development/MDTools/catdcd/
>
>
>
>
> On Tue, Jan 6, 2009 at 5:31 PM, <jouko_at_berkeley.edu> wrote:
>
>> I am trying to convert a dcd file that is larger than 7 GB to individual
>> pdb files. When I run the script I normally use to convert dcd files to
>> pdb files vmd aborts. The script is pasted below.
>>
>> mol load psf ubq_solution_wb.psf dcd ubq_wb.12ns.dcd
>> set nf [molinfo top get numframes]
>> for {set i 0} {$i<$nf} {incr i} {[atomselect top all frame $i] writepdb
>> /home/jouko/1ubq_phosphate5/0-3_ns/ubq_$i.pdb}
>>
>> I was thinking that the dcd file might be too large to be read by vmd,
>> so
>> I thought I could split it up using sed. However when I do that vmd is
>> not able to read the split up dcd files, except for the first one. Any
>> help would be appreciated.
>>
>>
>> Thanks,
>>
>> Jouko
>>
>>
>
>
> --
> Roman Petrenko.
> Physics Department
> University of Cincinnati
>