From: Lai, Jonathan (
Date: Thu Jan 14 2016 - 14:49:08 CST

Dear Albert,

As Josh was mentioning, you need to explicitly include the -s and -stype pdb flag.
Try the following:

catdcd -o output.pdb -otype pdb -mae m3-p2_9-out.cms -stype pdb -s "original PDB used to make the cms file"


From: [] on behalf of Albert []
Sent: Thursday, January 14, 2016 1:48 PM
To: Vermaas, Joshua V; vmd maillist
Subject: Re: vmd-l: pdb was not generated

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