AMBER Archive (2003)

Subject: Re: Proper Restraint usage

From: David A. Case (case_at_scripps.edu)
Date: Tue Apr 15 2003 - 16:04:50 CDT

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 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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