Re: AMBER: Bonds getting shorter in sander

From: Carlos Simmerling <>
Date: Fri, 1 Aug 2008 09:18:36 -0400

Pete- how was the bond energy in sander? you could run a 1 step min
and see if the
GMAX is one of the bond atoms. you might also use rdparm to check bond params
that are in your prmtop for that pair. is the short bond close to one of the K+?

On Fri, Aug 1, 2008 at 8:47 AM, Peter Gannett <> wrote:
> All:
> 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.
> Pete

Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
CMM Bldg, Room G80
Stony Brook University E-mail:
Stony Brook, NY 11794-5115 Web:
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Received on Sun Aug 03 2008 - 06:07:47 PDT
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