VMD-L Mailing List

From: Fotis Baltoumas (fbaltoumas_at_biol.uoa.gr)
Date: Fri Oct 03 2014 - 15:24:52 CDT

Hi,
Just create a selection containing only your membrane and store all its
index values in a file. It's pretty straightforward, with a little Tcl
scripting. An example would be this:

set membrane [atomselect top "resname POPC"]

set indices [$membrane get index]

set memFile [open membrane.ind w]

puts $memFile $indices

close $memFile

This little script will create a membrane.ind file, with indices
corresponding to POPC lipids, separated with whitespaces, compatible with
catdcd.

Hope I helped,
Fotis

> Hello,
>
> I would like to use catdcd to write POPC trajectory from water, following
> the example from the download website:
>
> http://www.ks.uiuc.edu/Development/MDTools/catdcd/
>
> catdcd -o eq_pro.dcd -i protein.ind eq01.dcd
>
> Takes only the coordinates corresponding to the indices in
> 'protein.ind' from eq01.dcd and writes them to eq_pro.dcd
>
> I supposed I will need an .ind file for my POPC. How will I create that?
>
> Thank you,
> Mihaela
>