VMD-L Mailing List

From: Robin Betz (robin_at_robinbetz.com)
Date: Thu Mar 08 2018 - 14:21:11 CST

Hi Wenze,

If you just want to visually hide the waters, use a representation with a
selection like "protein" or "all not water" to see just the protein.
More here under "Exploring different drawing styles": http://www.ks.uiuc.
edu/Training/SumSchool/materials/sources/tutorials/
01-vmd-tutorial/html/node2.html

The only reason to remove the waters from the trajectory entirely is if
you're having trouble fitting all of the frames into memory.
If you want the waters removed from the trajectory entirely, you can use
cpptraj, part of AmberTools (I'm guessing you're using AMBER
based on your mdcrd file).

cpptraj -p file.prmtop
trajin file.mdcrd
strip (:TIP3|:WAT) parmout file_nowat.prmtop
trajout file_nowat.mdcrd
go

Then visualise the new prmtop and mdcrd together.

Hope this helps,
Robin

On Thu, Mar 8, 2018 at 10:48 AM, Gu, Wenze <wenze_gu_at_brown.edu> wrote:

> Hi list,
>
> I have a mdcrd file with a protein and a lot of water molecules. I want to
> hide the water to see how the protein folds. However, I can only find
> tutorials for removing water in pdb. Does anyone know how to hide water in
> mdcrd file?
>
> Best,
> Wenze Gu
> Department of Chemistry
> Brown University
>