AMBER Archive (2006)

Subject: Re: AMBER: Dimer Image Wrapping

From: Melinda Layten (mlayten_at_gmail.com)
Date: Thu Mar 30 2006 - 12:16:06 CST

Thank you very much. This worked beautifully. And yes I searched and
didn't see it.

Thanks again,

Melinda Layten

On 3/30/06, Scott Pendley <scott.pendley_at_gmail.com> wrote:
>
> 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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