AMBER Archive (2008)

Subject: Re: AMBER: problem with zMatrix in tleap

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Fri Oct 31 2008 - 09:37:11 CDT

On Fri, Oct 31, 2008, WJ Ding wrote:

> I am trying to create the library for the residue which is LYS bonded
> (double bond) to an organic molecule with its NZ atom. What I did and the
> error display are as follows:
> > RET = createUnit RET
> > add RET ret
> > zMatrix RET {
> > { N H 1.010 }
> > { CA N H 1.444 118.271 }
> > { HA CA N H 1.089 108.273 175.797 }
> > { CB CA N H 1.507 113.478 -63.472 }
> > {2HB CB CA N 1.091 108.295 60.178 }
> > {3HB CB CA N 1.090 108.283 178.720 }
> > { CG CB CA N 1.511 111.845 -60.519 }
> > {2HG CG CB CA 1.090 109.182 -150.852 }
> > {3HG CG CB CA 1.090 109.135 -31.264 }
> > { CD CG CB CA 1.549 110.198 88.956 }
> > {2HD CD CG CB 1.090 106.075 -98.696 }
> > {3HD CD CG CB 1.090 106.026 17.554 }
> > { CE CD CG CB 1.532 116.237 139.443 }
> > {2HE CE CD CG 1.089 109.050 49.747 }
> > {3HE CE CD CG 1.090 109.047 169.214 }
> > { NZ CE CD CG 1.446 110.312 -70.571 }
> > { HZ NZ CE CD 0.999 115.715 -10.294 }
> > { C CA N H 1.494 105.755 58.005 }
> > { O C CA N 1.202 124.430 -37.457 }
> > { C1 NZ C25 C24 1.323 128.557 169.608 }
> > { H1 C1 NZ C25 1.069 117.330 179.067 }
> > { C2 C1 NZ C25 1.447 125.385 -0.850 }
> > { H2 C2 C1 NZ 1.070 119.061 9.565 }
> > { C3 C2 C1 NZ 1.349 121.910 -170.365 }
> ... # (I deleted some lines since it is too long. This part is just
> similiar to the above to define the other bonds, angles, and dihedral
> angles.)
> > }
> zMatrix: Argument #3 is type ?? Unknown type ?? must be of type: [atom]
> zMatrix: Illegal object in zMatrix entry. Entry was ignored
> zMatrix: Argument #4 is type ?? Unknown type ?? must be of type: [atom]
> zMatrix: Illegal object in zMatrix entry. Entry was ignored
> zMatrix: Argument #4 is type ?? Unknown type ?? must be of type: [atom]
> zMatrix: Illegal object in zMatrix entry. Entry was ignored

Does a smaller molecule work OK? Something like the example on p. 37 of the
Users' Manual? There might be some maximum size of z-matrices, but you should
certainly try to debug this by starting small and slowly adding atoms until
something breaks.

> >
>
> When I said "when I wrote the entry of zMatrix line by line", I mean that I
> input, for example, "{ N H 1.010 }", and then "{ CA N H 1.444
> 118.271 }", and then "{ HA CA N H 1.089 108.273 175.797 }"...
> Could you understand me now?

Sorry, I don't. Are you talking about having interactive input versus input
from an external file? Was what you input (typed?) different from what is
shown above? It is encouraging that things work one way, at least. But I
think we would need more information about what is really different when it
worked and when it did not.

If you don't figure it out, please try to post an actual example that fails
(as small as possible). Leaving out a bunch of lines makes it hard to
reproduce the problem, and just delays resolution: if we can't reproduce the
problem, we probably can't find the solution.

...dac

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