On Tue, Apr 15, 2003, Steve Seibold wrote:
> I am confused about what type of restraint I should use in AMBER. I have
> a heme cofactor bound through the iron to a nitrogen on the proximal
> histidine. When Leap processes the pdb they are not covalently linked
> and during MD they separate. That is, the bond length between iron and
> nitrogen reaches up to 3.0 angstroms.
You probably want a bond between these two atoms, not a restraint. Use
the "bond" command of LEaP to add the bond between the two atoms. Then they
will be covalently linked together (as in "real life").
...good luck...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
==================================================================
Received on Tue Apr 15 2003 - 22:53:01 PDT
