AMBER Archive (2002)

Subject: Re: Problem with LEAP

From: David A. Case (case_at_scripps.edu)
Date: Tue Jul 16 2002 - 10:19:24 CDT

On Tue, Jul 16, 2002, Miguel de Federico wrote:

> I'm trying to use tleap for preparing a simple molecule (cyclohexanol)
> and I get always the same error. I have revised the structure and seems
> OK. Could anybody help me about this?
>
>
> The error message is as follows:
>
> Bond: Maximum coordination exceeded on .R<c6a 1>.A<C06 6>
> -- setting atoms pert=true overrides default limits
> ATOMS NOT BONDED: .R<c6a 1>.A<H13 13> .R<c6a 1>.A<C06 6>
> !FATAL ERROR----------------------------------------
> !FATAL: In file [atom.c], line 443
> !FATAL: Message: bondAtomProblem found
> !
> !ABORTING.
>
>
> The prep file is:
>
> 0 0 2
>
> ciclohexanol axial
> molecule.res
> c5a XYZ 0
> CHANGE OMIT DU BEG
> 0.0000
> 1 DUMM DU M 999.000 999.0 -999.0 .00000
> 2 DUMM DU M 999.000 -999.0 999.0 .00000
> 3 DUMM DU M -999.000 999.0 999.0 .00000
> 4 C01 c3 M 5.021000 4.993000 0.328000 0.243673
> 5 C02 c3 M 4.533000 6.372000 -0.149000 -0.019753
> 6 C03 c3 M 5.767000 7.299000 -0.042000 -0.018652

..

This looks like a "prepc" file created by antechamber(?). In any event,
the order of atoms is wrong...in the tree structure, the hydrogen "E"
atoms must directly follow the carbon "M" atoms they are bonded to.

You could re-order the atoms, but the simplest thing to do is to use the
"prepi" option in antechamber; the "prepc" option is broken. We don't yet
have a bugfix to post, but I should try to post something that will warn users
of the problem.....

[We are moving antechamber/LEaP away from the (ancient) "prep" formats toward
mol2 as a general molecule interchange format, but that transition is not yet
completed.]

Thanks for your report. If you got the prep file by some other mechanism,
please let me know.

..regards....dave case 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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