VMD-L Mailing List

From: Ben Roberts (Ben.P.Roberts_at_vcp.monash.edu.au)
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
Ben

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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
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