From: Buddhadev Maiti (
Date: Thu Apr 05 2012 - 16:22:52 CDT

Dear Gianluca,

Sorry for my unclear email. My dcd file is very big 30GB and if I try to open, my computer freezes. That is why I am searching some tcl script to strip water and ions. Could you please help me.
Have a nice day,
From: Gianluca Interlandi []
Sent: Thursday, April 05, 2012 5:04 PM
To: Buddhadev Maiti
Cc: Jérôme Hénin;
Subject: Re: namd-l: DCD

Load your psf+dcd into VMD. Choose File -> Save Coordinates. In the text
field you can enter your atom selection, e.g., "not (water or ions)"


On Thu, 5 Apr 2012, Buddhadev Maiti wrote:

> Dear Jerome,
> I would like to make new dcd file from original dcd file (protein +
> membrane + water + ion) including only protein and membrane part without
> including any water and ions. Could you please reply me if there is any
> vmd tcl utilities, it will be great help for me. I am working with psf
> and dcd files.
> Have a nice day,
> Thanks,
> Maiti

Gianluca Interlandi, PhD
                     +1 (206) 685 4435

Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.

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