AMBER Archive (2006)

Subject: AMBER: Sander NOE violations

From: Andrew Box (box_twin3_at_hotmail.com)
Date: Thu Jul 06 2006 - 18:55:59 CDT

Dear Amber Users.

I am running nmr restraints during my dynamics runs in sander. When I look
for the NOE violations in the out put file generated, I notice I have
violations between atoms that have no constraints placed on them. Here is a
small part of my out put file:

     First atom Last atom curr. value target deviation penalty
------------------------------------------------------------------------------
  C24 BEN 13 -- C25 BEN 13: 1.500 1.800 0.300 1.799 d
0: 0
  C24 BEN 13 -- *O3 BEN 13: 5.992 4.600 1.392 22.845 d
0: 0
*O3 BEN 13 -- O4' DT 8: 5.370 4.080 1.290 20.802 d
0: 0
*O3 BEN 13 -- H3' DG 9: 5.573 5.330 0.243 1.178 d
0: 0
  H22 BEN 13 -- H1' DA 11: 5.438 4.970 0.468 4.377 d
0: 0
  H22 BEN 13 -- H3' DA 11: 4.946 4.610 0.336 2.262 d
0: 0
*H212 BEN 13 -- O4' DA 5: 5.223 4.970 0.253 1.285 d
0: 0
*H212 BEN 13 -- O4' DA 5: 5.223 4.800 0.423 3.586 d
0: 0
*H212 BEN 13 -- H4' DA 11: 4.878 4.150 0.728 9.568 d
0: 0
  H17 BEN 13 -- C2' DG 3: 4.481 3.060 1.421 23.422 d
0: 0

In the first line, it denotes a problem between two carbon atoms that are
connected with in aromatic ring. The second line shows a violation between
a carbon and oxygen atom that are separated by more than 8 covalent bonds
and have no NOE constraint between them. Also, I have no idea what the * in
front of the atoms names mean, as I have used no * in any atom names.

Thanks for any help.

Andrew Box

_________________________________________________________________
realestate.com.au: the biggest address in property
http://ninemsn.realestate.com.au

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