VMD-L Mailing List

From: Joshua Adelman (jla65_at_pitt.edu)
Date: Sun Feb 12 2012 - 08:38:22 CST

Hi Albert,

A couple of things:
1. The error catdcd is outputting is pretty clear: clickme.dtr is not an index file. If you want to use an index file, you should look at the documentation:
http://www.ks.uiuc.edu/Development/MDTools/catdcd/

which says:
-i <indexfile>
indexfile should contain the (zero-based) indices of the atoms in the
dcd files whose coordinates are to appear in the output file. The indices
should be ASCII text, separated by whitespace.

2. I don't think that catdcd will take a .cms as a structure file. I think you can use a .mae file, although I often just use a pdb.

3. Don't call catdcd on the clickme.dtr file directly. This holds true for vmd tcl commands like `animate read dtr` as well. You just want to call it on the directory containing the clickme.dtr file.

Try something like the following at it should work:

catdcd -o mytest.pdb -otype pdb -first 1 -last 2000 -s xxx.pdb -dtr MD_trj

Also be sure to use the catdcd distributed with VMD. At least in VMD 1.9 catdcd supports the desmond formats. I think the binary posted on the catdcd page does not.

Best of luck,
Josh

On Feb 12, 2012, at 3:23 AM, Albert wrote:

> Hello:
>
> I am going to extract Desmond MD frames by CATDCD into a single PDB file, here is my command:
>
> catdcd -o mytest.pdb -otype pdb -i MD_trj/clickme.dtr -first 1 -last 2000 -s MD-out.cms
>
> but it claimed:
> -----------log-------------
> CatDCD 4.0
> Reading indices from file 'clickme.dtr'
> Error: no indices found in file.
>
> Would you please give some advices?
>
> thank you very much