On Fri, 2015-02-06 at 21:02 +0200, Ibrahim Said wrote:
> Dear Daniel
> Thank you. I have run antechamber and have got Gdm.prepi file. Prepi file
>
> 0 0 2
>
> This is a remark line
> molecule.res
> Gdm INT 0
> CORRECT OMIT DU BEG
> 0.0000
> 1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
> 2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
> 3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
> 4 N1 nh M 3 2 1 1.540 111.208 -180.000 -0.516433
> 5 H11 hn E 4 3 2 1.000 43.383 -25.334 0.238367
> 6 H12 hn E 4 3 2 1.000 93.498 89.598 0.238367
> 7 C cz M 4 3 2 1.500 78.268 -161.170 0.298300
> 8 N3 nh B 7 4 3 1.500 109.483 -149.413 -0.500533
> 9 H31 hn E 8 7 4 1.000 109.518 -60.050 0.238367
> 10 H32 hn E 8 7 4 1.000 109.433 179.894 0.238367
> 11 N2 nh M 7 4 3 1.500 109.475 -29.346 -0.500533
> 12 H21 hn E 11 7 4 1.000 109.524 60.300 0.238367
> 13 H22 hn E 11 7 4 1.000 109.478 -179.686 0.238367
> 14 X 1 0 1 7.704 nan-10295.253 0.000000
>
>
> LOOP
>
> IMPROPER
> N2 N1 C N3
>
> DONE
> STOP
>
> Firstly, The chlorine ion disappeared. secondly, I do not know "What is
> nan?".
What it *is* is unimportant... it's what it's *not* that's important.
[1]
http://en.wikipedia.org/wiki/NaN
> Thirdly, When I ran parmchk, I got Segmentation fault (core dumped). I have
> tried to add -p but I got the same massage. Why does this massage appear?
Probably because of the NaN. What is that X atom supposed to be? Can
you delete it?
HTH,
Jason
[1] Not a Number: For one thing, it's not equal to anything... not even
itself
(In Python)
>>> nan = float('NaN')
>>> nan == nan
False
>>> nan != nan
True
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Feb 06 2015 - 11:30:04 PST
