AMBER Archive (2006)

Subject: Re: AMBER: Dimer Image Wrapping

From: Scott Pendley (scott.pendley_at_gmail.com)
Date: Thu Mar 30 2006 - 11:29:23 CST

Melinda,

I also work with dimers in TIP3P solvent truncated octahedron. This is a
script that I find very helpful. Similiar scripts can be found by searching
the archives. Assumes a homodimer composed of two 25 residue monomers.

trajin solvated.x
strip :WAT
strip :Na+
strip :Cl-
center :1-25 mass origin
image origin center familiar
center :1-50 mass origin
image origin center familiar
trajout strip.x
go

Have a great day,

Scott

On 3/29/06, Melinda Layten <mlayten_at_gmail.com> wrote:
>
> I'm getting inconsistent results in ptraj trying to get a non-covalently
> bonded dimer to center together when stripping water after an explicit
> solvent truncated octahedron run.
>
> Sample script:
>
> trajin solvated.x
> trajout strip.x nobox
>
>
> center :1-50 origin
> image :51-100 mass
> strip :101-9999
>
> go
>
> For a 50 residue monomer. I've tried lots of other combinations, but
> there is always some portion of the trajectory where the dimer interface is
> on the original box boundary.
>
> This is amber 8.
>
> Ideas?
>
> Melinda Layten
>

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