AMBER Archive (2006)

Subject: AMBER: Building Parameters

From: Steve Seibold (
Date: Mon Dec 11 2006 - 15:29:15 CST

Hello Amber

I am trying to build specific residues bound to metal in an enzyme. When
I tried to construct a topology file I got the "warning" that certain
dihedrals were missing and so I added them (not necessarily with the
correct force constants and angles at first) to see if I was successful
in removing the "warnings". For the most part this worked. However,
there are some dihedrals that are still not being recognized even though
I have written them into the force field parameters. I have put in bold
and underlined the first two dihedrals in xleap's print out labeled
"Check Enzyme.rft" and in my frcmod file, "Modfrcmod3.hemall. I do not
understand why these angles in my text are not being recognized in leap.
Can someone help me?


In addition there are several "improper" dihedral angles in the "Check
Enzyme" print out in leap also not recognized by leap e.g.
"NA-CA-CN-CB" and leap prints out this same improper dihedral multiple
times. Can someone explain to my why that is? Does it print the same
warning out every time it sees the same angle it doesn't recognize as it
scans through the enzyme parameters?



Thanks, Steve

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