AMBER Archive (2004)

Subject: Re: AMBER: CAP PROTOCOL SIMULATION

From: David A. Case (case_at_scripps.edu)
Date: Tue May 18 2004 - 17:47:26 CDT

On Mon, May 17, 2004, Ray Luo wrote:

> >may I ask which version of sander you use for "cap simulations"?
> >I would also be interested in the value of "cut".
> >
> >I am asking because I did get reasonable results with a cap and
> >sander8 only with an infinite cutoff, which made the calculations very
> >slow...
> >
> I meant sander8. There is no pb in previous versions of sander. If you
> use sander8 and "igb=10", "cut" will not be used, just set it to zero in
> case any memory allocation is invoked. A default _finite_ residue-based
> cutoff (cutres) of 12 A, atom-based cutoff (cutnb) of 10 A will be used
> for the pb simulation with cap.
>

I just want to augment Ray's response above by pointing people to section 5.16
of the Amber8 Users' Manual. The "cutoffs" mentioned above only serve to
separate the electrostatic interactions into a "direct" portion and a "grid"
portion (somewhat analogous to the PME separation between direct and
reciprocal terms). They are _not_ used to truncate the electrostic
interactions. Hence, you should expect to see behavior characteristic of an
infinite cutoff in previous versions of sander, with the added advantage of
including reaction field contributions from the continuum dielectric that is
outside the solvent cap. [Whether these igb=10 simulations are fast
enough for you is of course a separate matter, but they should be more
realistic than the cap simulations in previous versions, which truncated
long-range electrostatic interactions and had no reaction field component.]

> Note that the current pb implementation does not support partial
> solvation of a solute, i.e. cap on an active site of an enzyme only.

...regards...dac 

-- 

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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
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