From: Norman Geist (
Date: Mon Feb 16 2015 - 03:29:54 CST

There's a reason why the DCD is binary, this reason is, that it consumes
much less hard disk space. There's no non-binary dcd format, but other ascii
format trajectory files like rst7 from amber.


Norman Geist.


From: [] On Behalf Of
Sourav Ray
Sent: Monday, February 16, 2015 7:41 AM
To: Maxim Belkin
Subject: Re: vmd-l: Extracting coordinates from DCD file to a single PDB


on another note, is it possible to convert .dcd. file into ASCII format?


On Mon, Feb 16, 2015 at 12:01 PM, Sourav Ray <> wrote:

.psf file for defining the topology and .dcd file for the coordinates. it
would be convenient to get all the frames in a single pdb file as processing
will be much easier.




On Mon, Feb 16, 2015 at 11:21 AM, Maxim Belkin <> wrote:

What do you have as input (file format and content)?


On Feb 15, 2015, at 23:21, Sourav Ray <> wrote:


I guess there is some misunderstanding, I would like all the frames in a
single .pdb file, that too sequentially (frame 1, frame 2...). Is it
possible somehow?


On Fri, Feb 13, 2015 at 5:03 PM, Maxim Belkin <> wrote:

set nf [molinfo top get numframes]
set sel [atomselect top "protein"]
for {set i 0} {$i < $nf} {incr i} {
    $sel frame $i
    $sel writepdb "protein-$i.pdb"
$sel delete
mol delete top

If there are multiple proteins use more specific selection text, e.g. use
resids or something else.


> On Feb 13, 2015, at 04:09, Sourav Ray <> wrote:
> Hello
> I have been trying to extract all the frames of a protein into a single
PDB file. There is a code available currently in a thread here for
extracting each frame in different PDB files:
> set nf [molinfo top get numframes]
> for { set i 0 } {$i < $nf } { incr i } {
> set sel [atomselect top protein frame $i]
> $sel writepdb $i.pdb
> }
> Can someone please suggest a modification that works? Also, what if there
are multiple proteins? Can we extract each one separately?
> Regards
> Sourav