AMBER Archive (2008)

Subject: Re: AMBER: Error: Bond: Maximum coordination exceeded -- setting atoms pert=true overrides default limits

From: Ted Fischer (Origamisven_at_web.de)
Date: Tue Apr 15 2008 - 04:09:47 CDT

> > I am experiencing a problem with tleap setting up a system of multiple
> > solutes not connected to another. I am using a pdb file that I manually
> > edited in accordance to the syntax that was previously successful.
>
> Does the pdb file have a TER card in between each molecule? Other than that,
> we would need to have more information to be of much help. (e.g. what does
> the pdb contain? what LEaP commands did you use?)
>
> ...dac

Thanks for your effort, the TER cards are all in place...

I am treating methanol as a solute trying to construct a cubic box of n*n*n
equidistant molecules.

example pdb file (formatting may be broken):
**************************************************************************************
(Space)
ATOM 1 C1 MOH 1 -0.000 -0.000 0.000
ATOM 2 O1 MOH 1 1.087 0.906 -0.204
ATOM 3 HC1 MOH 1 -0.785 0.244 -0.653
ATOM 4 HC2 MOH 1 0.322 -0.981 -0.190
ATOM 5 HC3 MOH 1 -0.335 0.073 0.993
ATOM 6 HO1 MOH 1 1.317 1.324 0.629
TER
ATOM 7 C1 MOH 2 4.699 0.050 0.058
ATOM 8 O1 MOH 2 5.787 0.956 -0.146
ATOM 9 HC1 MOH 2 3.914 0.294 -0.596
ATOM 10 HC2 MOH 2 5.021 -0.931 -0.132
ATOM 11 HC3 MOH 2 4.365 0.123 1.050
ATOM 12 HO1 MOH 2 6.016 1.374 0.687
TER
(...)
*************************************************************************************

At this point the pdb file is still being manually edited to fit this format
(that works fine for 3x3x3), but I've double-checked the file and there don't seem
to be any deviations from the example above.

Now that I have scaled up the system using hundreds of methanol molecules in
a TIP3P waterbox I receive these errors:

tleap logfile
************************************************************************************
(...)
(Residue 101: MOH, Nonterminal, was not found in name map.)
(Residue 102: MOH, Terminal/last, was not found in name map.)
Joining MOH - MOH
Bond: Maximum coordination exceeded on .R<MOH 2>.A<HC1 1>
-- setting atoms pert=true overrides default limits
Joining MOH - MOH
Bond: Maximum coordination exceeded on .R<MOH 3>.A<HC1 1>
-- setting atoms pert=true overrides default limits
(...)
************************************************************************************

What ends up happening is that when I "tleap -f leaprc" the
displacement of solute molecules defined in the input.pdb structure, the output is
as expected up until a certain molecule when the error occurs and the symmetry in the output pdb is broken.

I have attempted to simulate with various large numbers of solute molecules without success,
always receiving the same error msg, while small systems seem to work just fine.

Any ideas are welcome...

Sven

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