VMD-L Mailing List

From: Ioana Cozmuta (icozmuta_at_mail.arc.nasa.gov)
Date: Wed May 24 2006 - 16:11:22 CDT

Hi John,

It goes through the all the files and for each it says
Opened file '1.xy' for reading
Read 0 frames from file 1.xyz, wrote 0

etc.
The final trajectory file is empty
All the files contain the same number of atoms in the same order and if
I load each individual file into VMD it shows just fine.

I don't have a similar set of pdb files at hand to try with catdcd for
the same purpose.

Best,
Ioana

John Stone wrote:
> Hi Ioana,
>
> Try this and see if it works for your XYZ files. I tried it on one of my
> XYZ files here and had a minor problem which I'm looking into, but it works
> fine for PDB and other types. It could be that I've got a bug to fix in the
> current version of the XYZ plugin. But try this and tell me if it works for
> you:
> catdcd -o new.dcd -xyz *.xyz
>
> for PDB:
> catdcd -o new.dcd -pdb *.pdb
>
> Note that the coordinate files will have to have consistent atom counts etc..
>
> John
>
> On Wed, May 24, 2006 at 01:38:54PM -0700, Ioana Cozmuta wrote:
>
>> Hi John,
>>
>> Thank you for the link. Say I have a series of xyz files 1 through 1000
>> what is the correct syntax and the best way to use catdcd to generate
>> the dcd file?
>>
>> Ioana
>>
>> John Stone wrote:
>>
>>> Try the latest version of CatDCD, which should be able to read the XYZ
>>> file and turn it into a DCD for you:
>>> http://www.ks.uiuc.edu/Development/MDTools/catdcd/
>>>
>>> John Stone
>>> vmd_at_ks.uiuc.edu
>>>
>>>
>>> On Tue, May 23, 2006 at 04:55:51PM -0700, Ioana Cozmuta wrote:
>>>
>>>
>>>> Hi vmd users,
>>>>
>>>> I have a series of .xyz files as snapshots of a trajectory. Is there an
>>>> easy and quick way to turn this into a .dcd trajectory file?
>>>>
>>>> thank you,
>>>> Ioana
>>>>
>>>>
>>>
>>>
>> --
>> Ioana Cozmuta, Ph.D
>> Eloret Corporation
>> NASA Ames Research Center
>> Mail Stop 230-3
>> Moffett Field, CA 94035
>> phone (650) 604-0993
>> e-mail: icozmuta_at_mail.arc.nasa.gov
>> http://people.nas.nasa.gov/~ioana/
>>
>
> 

-- 
Ioana Cozmuta, Ph.D
Eloret Corporation
NASA Ames Research Center
Mail Stop 230-3
Moffett Field, CA  94035
phone (650) 604-0993
e-mail: icozmuta_at_mail.arc.nasa.gov
http://people.nas.nasa.gov/~ioana/