AMBER: Bonds getting shorter in sander

From: Peter Gannett <>
Date: Fri, 01 Aug 2008 08:47:02 -0400

I have a strange problem. We've been trying to run an MD on a G-quadruplex. The structure was from the NDB and is more or less four of the human telomer repeat (TTAGGG)4 (minus a TT). It also has 3 K+, two intercalated. The pdb was solvated and neutralized. A MM run was done on the solvent with the solute restrained. To this point, everything is fine except for a few close contacts according to xleap. Next, an MM with no restraints was run and at the end of the run, though it completed with out complaining, xleap reports that a bond in one of the thymidines has decreased to 0.48 angstroms. The output of the unit editor in xleap is below:
Unit Editor: WARNING: There is a bond of 0.476645 angstroms between:
Unit Editor: ------- .R<DT 11>.A<N3 23> and .R<DT 11>.A<C2 25>
Unit Editor: WARNING: The unperturbed charge of the unit: -19.000000 is not zero.
Unit Editor: Warning: Close contact of 1.721330 angstroms between .R<DT 5>.A<C2 25> and .R<DT 5>.A<H3 24>
Unit Editor: Warning: Close contact of 1.735185 angstroms between .R<DT 6>.A<C2 25> and .R<DT 6>.A<H3 24>
Unit Editor: Warning: Close contact of 1.664213 angstroms between .R<DT 11>.A<C2 25> and .R<DT 11>.A<H3 24>
Unit Editor: Warning: Close contact of 1.724770 angstroms between .R<DT 12>.A<C2 25> and .R<DT 12>.A<H3 24>
Unit Editor: Warning: Close contact of 1.754660 angstroms between .R<DT 17>.A<C2 25> and .R<DT 17>.A<H3 24>
Unit Editor: Warning: Close contact of 1.736804 angstroms between .R<DT 18>.A<C2 25> and .R<DT 18>.A<H3 24>
We have tried to avoid this problem by removing restraints more slowly but with no success.
I am a bit mystified as to why sander would think it was a good idea to shorten a bond by about an angstrom. Has anyone ever seen this before? Any suggestions for a solution? Thanks.

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Received on Sun Aug 03 2008 - 06:07:46 PDT
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