VMD-L Mailing List

From: amin_at_imtech.res.in
Date: Tue Mar 18 2014 - 12:03:26 CDT

 

Hi. Assuming you want to get protein alone, I think you can use
something like

mol load psf name.psf pdb name.pdb
set all [atomselect top "all"]

set sel [atomselect top "protein"]
$sel writepsf protein.psf
$sel writepdb protein.pdb

set indices [$sel get index]

set file [open protein.ind w]

foreach i $indices {

 puts $file $i

}

flush $file

close $file

On 2014-03-18 18:31, Ramin Ekhteiari wrote:

> Hi ,
>
> I have a big dcd file, so I would like to remove the water molecules from my dcd file and create a new one by using catdcd, but I think I should create a index file first to do such a thing,.
>
> would you please advise me on how to do this.
>
> Would be grateful for any advice.
> Cheers,
> Ramin.