From: Ben Roberts (
Date: Thu Jul 22 2004 - 20:27:18 CDT

Hi Axel

Thanks for your help with this, based on your suggestions I have been able
to write a short Tcl script to extract frames as PDB files.

In case anyone else would like this information, the script follows:

animate goto start

set num_frames [molinfo top get {numframes}]

for {set frm 1} {frm <= $num_frames} {incr frm} {

        animate goto $frm

        animate write pdb frame_$frm.pdb beg "$frm" end "$frm" top


I have found that the unit cell information present in the DCD file is
automatically included in the PDB file - if, and only if, a single step is
included in the PDB. It was broken because I was trying to write out
multiple steps.

Thanks for your help, and I hope this info is useful to someone.

Best regards

Benjamin P. Roberts, B.Sc.(Hons)
Ph.D. Student

Department of Medicinal Chemistry
Victorian College of Pharmacy (Monash University)
381 Royal Parade, Parkville VIC 3052, Australia

Phone +61 3 9903 9674 | Fax +61 3 9903 9582 | Mobile +61 401 784 940