AMBER Archive (2002)

Subject: Re: How to decrease the solvated system in Amber6?

From: Ling Zhang (lz267_at_nyu.edu)
Date: Tue Jul 02 2002 - 10:30:19 CDT

Hi,

Thanks for so many help from you these days.

The LEaP command I used is;

solvateOct x WATBOX216 10.0

And I got a solvated system around 80,000 atoms after that. And I
wandered whether I could further decrease the system by treating the
350 crystal water molecutes as the solvent. Could you give me some
suggestion on that? Thanks again.

Best,
Ling

----- Original Message -----
From: "David A. Case" <case_at_scripps.edu>
Date: Tuesday, July 2, 2002 7:38 am
Subject: Re: How to decrease the solvated system in Amber6?

> On Mon, Jul 01, 2002, Ling Zhang wrote:
>
> >
> > I tried to decrease my solvated system by using a trucated
> octahedral
> > box in Leap of Amber6. But the result is still not satifactory.
> Could
> > you give me some suggestions in decreaseing the system without
> > affecting the quality of the simulation? Thanks a lot.
>
> Without knowing how big your box was, or what was "not
> satisfactory", it
> is hard to give much advice. Here is the LEaP command I usually use:
>
> solvateOct x WATBOX216 12.0 0.75
>
> You could compare that to what you use. Note that I have never
> simulatedsomething as large as a 900 residue protein in water (nor
> have many other
> people, I imagine): you are trying something rather difficult, and
> shouldexpect things to require lots of computer time and patience.
>
> ..hope this helps...dac
>
> --
>
> ==================================================================
> David A. Case | e-mail: case_at_scripps.edu
> Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
> The Scripps Research Institute | phone: +1-858-784-9768
> 10550 N. Torrey Pines Rd. | home page:
> La Jolla CA 92037 USA | http://www.scripps.edu/case
> ==================================================================
>
>