Tutorial-l Mailing List

From: Mai Suan Li (masli_at_ifpan.edu.pl)
Date: Fri Dec 01 2006 - 20:18:02 CST

Dear Tim
I have fixed that problem which is exactly the
same as you described in this email.
Anyway, thank you very much.

I still have a big problem with constant-force simulation
in droplet. I really don't know why some water molecules escape
from the droplet. I have written to your crew about two weeks ago
but I did not get any answer. If you have some time for this problem,
I'll describe you in more detail.
Have a nice weekend. Li

On Fri, 1 Dec 2006, Timothy Isgro wrote:

> 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
> writepdb:
>
> [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?
>
> -Tim
>
>
> 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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