From: Timothy Isgro (
Date: Fri Dec 01 2006 - 14:45:09 CST

Hi Li,
The easiest way to do extract pdb coordinates from a dcd file is to
simply load the system in VMD and use the atomselect command with

[atomselect top "XXX" frame N] writepdb newfile.pdb

Here, XXX is the part of your system you want to write to the pdb,
and N is the frame of the dcd whose coordinates you want to write.
XXX=protein to write all proteins to a pdb, XXX='protein or water' to
write proteins and water, XXX=all to write the entire system. I'm
not sure about the script you're talking about.

I think the only need for a script here would be to write many
multiple selections or frames to a pdb.

Does that help?


On Nov 25, 2006, at 8:25 PM, Mai Suan Li wrote:

> Hello, every one
> I have the script file to get the pdb coordinates for protein
> from dcd file. However I don't know how to extract
> pdb coordinates for the whole system (protein + water).
> I would appreciate very much if some one can help me with this.
> Best regards, Li
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