VMD-L Mailing List

From: Albert (mailmd2011_at_gmail.com)
Date: Thu Jan 14 2016 - 13:48:28 CST

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