AMBER Archive (2008)

Subject: Re: AMBER: problem with zMatrix in tleap

From: WJ Ding (dingwanjian_at_gmail.com)
Date: Fri Oct 31 2008 - 10:48:27 CDT

2008/10/31 David A. Case <case_at_biomaps.rutgers.edu>

> 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.

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. (I think you mean this one.
:-))

>
> > >
> >
> > 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
>

The whole stuff is quite long, which I put it in the attachment (is it
ok?). I did this with tleap.

The attached file started from the very beginning what I did. The lines with
">" are what I typed, and those without ">" are the output. Hope you can
understand this.

thanks a lot.

WJ

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