From: Richard Wood (
Date: Thu Jan 14 2016 - 15:25:28 CST

Mae files are Schrodinger files and should be convertible using Maestro (where mae comes from).

From: [] on behalf of Josh Vermaas []
Sent: Thursday, January 14, 2016 1:41 PM
To: Albert; vmd maillist
Subject: Re: vmd-l: pdb was not generated

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

On 01/14/2016 11:53 AM, Albert wrote:
> Dear:
> I am using catdcd to convert a .mae file into .pdb file with command:
> catdcd -o input.pdb -otype pdb -stype mae -s m2-anta_9-out.cms
> However, after I run this command no any pdb file was generated. I
> didn't get any error information in my terminal. I am just wondering
> what's happening?
> thank you very much
> Albert