VMD-L Mailing List

From: Gu, Wenze (wenze_gu_at_brown.edu)
Date: Thu Mar 08 2018 - 15:31:44 CST

Thank you! It works!

Best,
Wenze Gu
Department of Chemistry
Brown University

On Thu, Mar 8, 2018 at 3:21 PM, Robin Betz <robin_at_robinbetz.com> wrote:

> 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
>>
>
>