Dear David,
Thank you for your reply. I used ambpdb to convert .prmtop and inpcrd to
.pdb, and visualize .pdb using vmd.
I can see the entire waterbox by selecting resname WAT using VMD. The
protein is in the water box.
Thanks again!
Wu
-----Original Message-----
From: David Cerutti [mailto:dscerutti.gmail.com]
Sent: Saturday, March 12, 2016 5:58 PM
To: AMBER Mailing List
Subject: Re: [AMBER] TIP3P
First of all it seems like you told VMD that it is reading an Amber Parm7
topology and Amber coordinates (.crd). However, you need to tell cmd that
it is reading coordinates WITH periodic box--I think that will get rid of
the yarn ball. Otherwise, because it's a periodic box, and a VERY
generous
buffer volume, I think you're just seeing a large and loose protein in the
best representation VMD can make--it probably is surrounded by water when
you consider periodic boundaries, but you will see that only if you center
the box on an appropriate residue of the protein.
On Mar 12, 2016 2:12 PM, "Wu Xu" <wxx6941.louisiana.edu> wrote:
> Dear Amber users and developers,
> I used xleap (Amber 12) to solvate a protein (786aa) inside a TIP3PBOX
> 20.0. I found only part of the protein is in the water box (a picture is
> attached). Is there any way to solve this problem? Thanks in advance,
> Wu Xu
> Department of Chemistry
> University of Louisiana at Lafayette
>
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>
>
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Received on Sat Mar 12 2016 - 17:00:03 PST
