AMBER Archive (2008)

Subject: Re: AMBER: problem with zMatrix in tleap

From: WJ Ding (dingwanjian_at_gmail.com)
Date: Fri Oct 31 2008 - 09:23:45 CDT

Thank you very much first.
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
>

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?

Do you have any idea about this? Thank you so much.

WJ

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

> On Fri, Oct 31, 2008, WJ Ding wrote:
> >
> > "zMatrix: Argument #3 is type ?? Unknown type ?? must be of type: [atom]
> > zMatrix: Illegal object in zMatrix entry. Entry was ignored"
> >
> > I have no idea about this problem. But when I wrote the entry of zMatrix
> > line by line, there was no error display.
>
> This is an example of a type of question we get rather too often: you list
> an error message, but nothing about what input you used that led to this
> message. It is almost never possible to provide useful help in such
> circumstances.
>
> Also, the phrase "when I wrote the entry of zMatrix line by line" is
> confusing. Try to be very explicit about *exactly* what you did that
> caused
> the problem.
>
> ...thanks!...dac
>
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