Re: [AMBER] Umbrella Sampling with Z-axis as Reaction Coordinate

From: Dail Chapman <>
Date: Sun, 14 Oct 2012 22:23:00 -0700

Thank you, Jason, for your help. I would need to use the center of mass of the membrane. Can this be defined in terms of center of a plane of c.o.m.s of residues? Or is this restricted to c.o.m.s of atoms? For example, say the membrane consists of 80 phospholipids (i.e., residues 1-80) and your small molecule is residue 81. Basically we want to know two things:

(1) If we can use whole residues instead of just atoms for the "natural language" restraint specification:
restraint = "angle(plane(com(:1-20),com(:21-40),com(:41-60),com(:61-80)),com(:81))"

(2) Where does one put this restraint definition? In the main input file or in a secondary restraint (e.g., DISANG) file?

If anyone has any suggestions, it would be really helpful. Thanks, -Dail

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Received on Sun Oct 14 2012 - 23:30:08 PDT
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