VMD-L Mailing List

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Fri Feb 10 2012 - 07:29:36 CST

>
> Is it possible to run VMD in stand-alone (non-graphical) mode ? Within a
> script, I just want to be able to read a .coor NAMD binary file and save it
> as an ASCII
> .pdb file for further use in NAMD.
>
> Indeed it's possible:
use vmd -dispdev text -e "path to script to load and save your stuff"

More info here:
http://www.ks.uiuc.edu/Research/vmd/current/ug/node207.html

You could also consider using catDCD for this.
http://www.ks.uiuc.edu/Development/MDTools/catdcd/

An alternative question is, how can I get NAMD to write a .pdb file
> after an MD ? I tried writepdb <filename> in an NAMD script and it gives
> the following error:

 Try *binaryoutput no*
More info here
http://www.ks.uiuc.edu/Research/namd/2.8/ug/node13.html#SECTION00062200000000000000

Regards,
Ajasja