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.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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Received on Tue Aug 26 2003 - 01:53:01 PDT
