Re: Saving coordinates of each frame into one separate .pdb file from a 100-frame .dcd file.

From: Joshua D. Moore (jdmoore_at_unity.ncsu.edu)
Date: Sat Jan 21 2006 - 18:32:58 CST

I think the new catdcd4.0 can also do this. I haven't tried it, but it
says that it can take dcd as input and write pdb as output.

Josh

On Sat, January 21, 2006 1:54 pm, Boyang Wang wrote:
>
> Thanks. We also did another script yesterday, as follows, and I guess that
> there are other ways too.
>
> for {set i 1} {$i < 99} {incr i} {
> [atomselect top all frame $i] writepdb $i.pdb
> }
>
>
> Carlos Simoes <caze.mailings_at_gmail.com> д Hi,
> I intended to do exactly the same, some time ago, and I found this
> way, back then:
> 1- Load your entire trajectory on VMD (psf+dcd);
> 2- Use the "Save Coordinates" tool (here you can select a part or the
> whole system to be saved);
> 3- Use the attached "splitmultiframepdb2files.tcl" script to split the
> single multi-framed pdb file you obtain from the previous step (take a
> look to the script to check its usage).
>
> I hope this helps...
>
> carlos
>
>
> On 1/20/06, Boyang Wang
> wrote:
>> Hi all, I am wondering what is the best way to save the coordinates of
>> each
>> frame into one separate .pdb file from a 100-frame .dcd file.
>>
>> What I can do now is to save each frame as one pdb file using VMD, and
>> I
>> can only do this one frame by one frame. This is very slow.
>>
>> Thanks for all your time.
>>
>> Boyang.
>>
>>
>> ________________________________
>> Ż1Gٷְٷ
>> Ż-ɱɧ
>>
>>
>
>
>
>
>
> Boyang Wang,
> Email - bwang9_at_uic.edu
> Major - Phys. Chem.
> dept Chemistry,
> Univ Illinois, Chicago,
> 60607 IL US.
> __________________________________________________
> ϿעŻ?
> http://cn.mail.yahoo.com

--------------------------------------------------
Joshua D. Moore
Graduate Student
North Carolina State University
Department of Chemical and Biomolecular Engineering
Box 7905 Centennial Campus
Engineering Building I
911 Partners Way
Raleigh, NC 27695-7905
Phone: (919) 513-2051
Fax: (919) 513-2470
Email: jdmoore_at_unity.ncsu.edu
--------------------------------------------------

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