AMBER: a challenge: a periodic box that cuts through a monomer

From: Kenley Barrett <>
Date: Mon, 20 Mar 2006 16:06:49 -0600

Dear AMBER community,

I'm struggling with a problem right now that I was hoping some of you might
have insights on. A member of my research group used AMBER to simulate an
infinite helix of DNA. Basically, he read the repeat unit of DNA into XLeap,
created a solvent periodic box, and then manually changed the size of the
periodic box in the .inpcrd file to create a periodic box that was exactly
the length of the repeat unit. Thus when periodic boundary conditions were
implemented he got an infinite helix. I want to do the same thing, but
instead of DNA I am working with a polymer of protein monomers. The geometry
of the protein helix is such that if I create a periodic box that is the
length of the repeat unit of the polymer, the box inevitably cuts through
the middle of a monomer at each end of the box. This is a major problem. I
tried doing what my colleague did, by just changing the length of the box to
the length of the repeat unit by modifying the .inpcrd file. This didn't
work--I recieved a bunch of NaNs in my output:

 NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
 Etot = NaN EKtot = 0.0000 EPtot = NaN
 BOND = 116102.5123 ANGLE = 28536.2731 DIHED =
 1-4 NB = 5621881.6022 1-4 EEL = 240772.1616 VDWAALS = NaN
 Ewald error estimate: NaN

Reading an exact repeat unit into XLeap won't work either, because again,
the repeat unit would have to have monomers that are cut in half at each
end, and XLeap would ruin things by completing the residues. Even if XLeap
didn't complete the residues, I'm assuming that it wouldn't know how to
create a .prmtop file for a protein with residues that are cut in half. I am
stumped. Does anyone have any suggestions on how I can trick AMBER into
working with a periodic box that cuts through a monomer?

Thank you very much in advance for any suggestions.


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Received on Sun Mar 26 2006 - 06:10:08 PST
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