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I have a set of dcd files that I want to concatenante to have one (long) dcd file. I put in a VMD Tkconsole (VMD version : 1.9.2) the following code :

catdcd -o output.dcd -i indexFile.ind input1.dcd input2.dcd input3.dcd

and I had the following error : 

wrong # args: should be "catdcdList dcdFileNames outFile indexFile stride"

so I wrote :

catdcdList -d input1.dcd input2.dcd input3.dcd -o output.dcd -i indexFile.ind -s 1

Even though the catdcdList command is reckognized (colored in green), I still have exactly the same error message. I tried out littles changes to my request but I keep getting the above error message. The second example from the official catdcd webpage does not work neither.

dexterdev
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dada
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  • Looks like it wants the first argument to be a list, and no options: `catdcdList {input1.dcd input2.dcd input3.dcd} output.dcd indexFile.ind 1` – glenn jackman Jul 16 '15 at 13:38
  • This doesn't work neither. I tried to put the remaining files between embraces, still doesn't work. – dada Jul 21 '15 at 11:16
  • I reinstalled the vmd package. Now catdcd is recognized. However, when I type `catdcd input1.dcd input2.dcd -o test.dcd `, I have this error : `Error: input2.dcd exists already. catdcd will not be run because that would append to this file.` – dada Jul 21 '15 at 11:39

1 Answers1

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I have been having the same issue with catdcd on my ubuntu 15.10 laptop.

In order to get it to work, I added the catdcd directory to my PATH.

How to do this (note, my instructions add catdcd permanently to PATH):

1) Go to /home/user directory. Using ls -a command you should see a file called .bashrc (don't forget the "."; it's important and means that the file is a hidden file).

2) Open .bashrc using gedit (or a similar text editor). If you want, you can make a backup of .bashrc (cp .bashrc ./.bashrc_bkup for example).

3) At the end of .bashrc, append this:

export PATH="/usr/local/lib/vmd/plugins/LINUXAMD64/bin/catdcd5.1:$PATH"

This directory is the default that is installed when you configure VMD 1.9.2. Note that you may have a different version of catdcd installed (such as catdcd4.0, which comes from the VMD website). In any case, you'll need to find the directory that corresponds to the catdcd file on your computer.

4) Close and open the terminal again. Type $PATH command to make sure this directory is now present.

5) You should be able to type "catdcd" in the terminal (without opening vmd) and it should now recognize the command. You should also be able to use catdcd in the tkconsole, but I find it easier to use in the terminal.

PeaWagon
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