VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Thu Jan 14 2016 - 13:55:15 CST

Ahh. Ok. Well then give it both:

catdcd -o output.pdb -otype pdb -stype mae -s m3-p2_9-out.cms -mae
m3-p2_9-out.cms

Its worth mentioning that VMD can do this same operation as a two line
script:

mol new m3-p2_9-out.cms type mae
animate write pdb output.pdb

-Josh

On 01/14/2016 01:48 PM, Albert wrote:
> Hi Josh:
>
> I tried command:
>
> catdcd -o output.pdb -otype pdb -mae m3-p2_9-out.cms
>
> but it failed with messages:
>
> CatDCD 5.1
> Cannot write timesteps in 'pdb' format without structure file.
>
>
>
>
> On 01/14/2016 08:41 PM, Josh Vermaas wrote:
>> Hi Albert,
>>
>> You gave it a structure, but no input file. I'm not sure what a
>> mae-type file contains, but have you tried doing it this way?
>>
>> catdcd -o output.pdb -otype pdb -mae m2-anta_9-out.cms
>>
>> The -stype and -s flag are there so you can add in additional
>> topological information (bonds) not present in the input files (like
>> a dcd) that the output file type (say a js) can contain. The standard
>> -<filetype> inputfile arguments are there for geometrical information
>> like where atoms are located in space.
>>
>> -Josh Vermaas
>