From: JC Gumbart (
Date: Sun Feb 12 2012 - 08:34:56 CST

Again, -i is used for an index file NOT the input file. Use “-dtr MD_trj/clickme.dtr “. You’ll also need to specify “-stype”; I think “mae” will work for cms files?


From: [] On Behalf Of Albert
Sent: Sunday, February 12, 2012 8:24 AM
To: JC Gumbart
Cc: vmd maillist
Subject: Re: vmd-l: problem with catdcd


  than you very much for kind messages.
  I am trying to extract DESMOND MD simulation files and I don't think there would be any PSF/PDB file from Desmond output. It only contains clickme.dtr and MD-out.cms files which I specified in the command:

catdcd -o mytest.pdb -otype pdb -i MD_trj/clickme.dtr -first 1 -last 2000 -s MD-out.cms

I DO type catdcd to get help from CATDCD for help but there is no more comments for Desmond. So, I am turning to this maillist for helps.


On 02/12/2012 03:21 PM, JC Gumbart wrote:

While –i for input may be intuitive, it’s actually used for an index file. Try typing just “catdcd” at the command line to see the correct way to use it. Note that you will also need to give it a PSF/PDB file as well.