Dears,
I am sorry for confusion. x item should be a chlorine ion and when
calculate the charges using antechamber I got the previous prepi file.
Please, can I calculate the charges of guanidine and then add Cl ion in
xleap.
thanks
said
On Fri, Feb 6, 2015 at 9:19 PM, Jason Swails <jason.swails.gmail.com> wrote:
> 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 Sat Feb 07 2015 - 00:30:02 PST
