Re: Proper Restraint usage

From: David A. Case <>
Date: Tue, 15 Apr 2003 14:04:50 -0700

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:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
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Received on Tue Apr 15 2003 - 22:53:01 PDT
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