AMBER Archive (2008)

Subject: Re: AMBER: problem with zMatrix in tleap

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Sun Nov 09 2008 - 11:17:02 CST

On Fri, Oct 31, 2008, WJ Ding wrote:
> 2008/10/31 David A. Case <case_at_biomaps.rutgers.edu>
>
> Yes. it works well when I did the same to a small molecule. I just copied
> the example H2O of P47 of Amber9 User's Manual.

If you really want to go this way (build a very large molecule using a
zMatrix), you will probably have to build ever-larger molecules slowly, to try
to use divide-and-conquer to find the error. The only thing I saw was a typo
here:

> {C19 C18 C17 c16 1.500 114.518 -45.470 }

That could lead to the sort of error you report, although I don't understand
the details.

It might be easier to use some other tool to add hydrogens to your original
pdb file (even xleap!), then use antechamber to create the library you need.
As you can see, when the zmatrix fails, the error messages don't directly
point to exactly which line is wrong...

...good luck...dac

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