Re: [Apbs-users] plot density of charge

[Yong H. <yhu...@gm...>]

Hi Davide,

I am guessing you are using a pre-1.1.0 version of APBS? This density.py has
been removed since 1.1.0 release. Also, can you send us related files so
that we can recreate such a problem?

Thanks,

Yong


On Wed, Aug 5, 2009 at 11:53 PM, Davide Mercadante <
dm...@au...> wrote:

> Dear Dr. Nathan Baker,
>
> in addition to my other mail I want to ask also about the qdens.dx
> plotting. I tried to use the script in the apbs density.py to plot the qdens
> that came out from my calculation (from qdens.dx to qdens.dat) However, the
> creation of the file qdens.dat gives me this wrong output:
>
> 1.0 7.8098526426e-06 4.90707513752e-05
> 2.0 9.08592800744e-06 0.000163247890092
> 3.0 1.74064881537e-05 0.000491352461942
> 4.0 2.86399407285e-05 0.00121115268108
> 5.0 3.37812484028e-05 0.00227242189919
> 6.0 3.76921540481e-05 0.00369338263026
> 7.0 4.94599244839e-05 0.00586874372594
> 8.0 5.36104209604e-05 0.00856349740026
> 9.0 6.96500765029e-05 0.0125021164362
> 10.0 0.000108781773269 0.0193370768311
> 11.0 0.000125319522043 0.0279985404068
> 12.0 0.000123175997222 0.0372857917981
> 13.0 0.00010861181144 0.0461573575898
> 14.0 0.00012477201506 0.0571328772747
> 15.0 0.000113271941683 0.0678085062701
> 16.0 0.000111392095609 0.0790068611256
> 17.0 0.000109050604748 0.090655008803
> 18.0 0.000150059278433 0.107626313365
> 19.0 0.000156427679157 0.126300731176
> 20.0 0.000149383020766 0.145072755201
> 21.0 0.000173464776641 0.167960893255
> 22.0 0.00015784244754 0.189779466894
> 23.0 0.000132089797766 0.208868194455
> 24.0 0.000117920051609 0.226650119311
> 25.0 0.000105373624709 0.243202169574
>
> Traceback (most recent call last):
>   File "density.sh", line 308, in <module>
>     if __name__ == "__main__":  main()
>   File "density.sh", line 301, in main
>     qsum = qsum + vgrid.value((x, y, z))
>   File "density.sh", line 140, in value
>     + (1.0-dx)*(1.0-dy)*(1.0-dx)*self.data[self.ijk2u((ilo,jlo,klo))]
>   File "density.sh", line 86, in ijk2u
>     raise IndexError, errstr
> IndexError: Index element 0 (130) out of range!
>
> Please, can you tell me if I have to change something in the script or if
> something in my qdens.dx file is wrong? I have visualized the qdens.dx file
> using vmd ans all seem to be fine.
>
> Thanks in advance for any help.
>
> Cheers,
> Davide
>
>
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-- 
Yong Huang, D.Sc.

Center for Computational Biology
Washington University School of Medicine