Proper Restraint usage

From: Steve Seibold <>
Date: Tue, 15 Apr 2003 16:42:59 -0400

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.
I have been able to use position restraints on the iron of the heme and
nitrogen of the proximal histidine using the NTR = 1 variable and
defining atom types in the input files. This is keeping the distance
between the two atoms close so far now. But this is really a position
restraint of the separate atom's xyz coordinates and not a distances
restraint between the two atoms.Right?

Am I enforcing the restraint correctly? Should I be using &rst?

Thanks, Steve
Received on Tue Apr 15 2003 - 21:53:01 PDT
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