AMBER Archive (2003)

Subject: Re: AMBER: The FCAP parameter in amber7

From: David A. Case (case_at_scripps.edu)
Date: Mon Aug 25 2003 - 18:59:45 CDT

On Fri, Aug 22, 2003, Thomas Steinbrecher wrote:
>
> As suggested there I added FCAP=1 to my input file for
> sander. I thought that would place a small (1
> kcal/(mol*A*A)) restraint on my cap waters fixing them
> close to their starting places.

No. The "cap" option only adds a penalty if the distance of any water from
the (xcap,ycap,zcap) point exceeds cutcap. There are no forces on most of the
waters, only ones that go outside the cap.

> Indeed the simulation runs fine for some 100ps now, but
> when I look at the rmsd, it is quite stable at ~1.3 A for
> my ligand and protein as expected (or hoped at least) but
> for the water molecules the rmsd is rising constantly.

This sounds OK.

> the restraint energy is 0 in my output files.

The capwat() function (in ene.f) adds the force outlined above, but does
not add anything to the energy. This is arguably a design flaw, but is
consistent with the behvior you see.

..hope this helps...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:                   
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