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

-- 

================================================================== 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 ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber_at_scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu