AMBER Archive (2009)

Subject: Re: [AMBER] water bonding with protein

From: David A. Case (
Date: Wed Apr 15 2009 - 06:58:17 CDT

On Tue, Apr 14, 2009, Mark M Huntress wrote:

> Hi, I have a protein that I am running MD on, and it comes with 300
> water molecules in the pdb. After I generate a prmtop file, I open my
> pdb file in VMD, and it says that there are unnatural bonds between the
> water and the protein. Is this just because the waters are close to the
> protein in the pdb file? Or when I generated the prmtop file, did it
> parameterize my system with these unnatural bonds? I mean, when I run
> the MD with my prmtop file, will it run as if the waters are bound to
> the protein? Should I worry about this?

If you load the prmtop file in VMD, it will display the bonds that are
actually in the prmtop file, and not try to create bonds based on
distances. So, you can easily check for yourself.

That said, LEaP will not create bonds between protein and water molecules,
unless you specifically asked for them..


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