[gmx-users] Insane.py problem

[Carlos Navarro Retamal]

I have no idea either.
with:
./insane.py -f PSII-CG.pdb -pbc square -box 25,20,15 -l CPG:0.5557 -l PPG:0.0543 -l CDGDG:2.56 -l CMGDG:4.35 -l CSQDB:2.4774 -l CSQDG:0.0026 -sol W -o system.gro
works perfectly.
Best,
carlos

--
Carlos Navarro Retamal
Bioinformatics Engineering
Ph. D (c) Applied Sciences.
Center of Bioinformatics and Molecular Simulations. CBSM
University of Talca
Av. Lircay S/N, Talca, Chile
T: (+56) 712201 798
E: carlos.navarro87 at gmail.com or cnavarro at utalca.cl



On May 13, 2015 at 3:45:24 PM, João Henriques (joao.henriques.32353 at gmail.com<mailto:joao.henriques.32353 at gmail.com>) wrote:

That's strange. x = [ float(i) for i in a.split(",") ] + 6*[0] creates a
list x that is [20.0, 20.0, 10.0, 0, 0, 0, 0, 0, 0]. There should be no
error for having an empty space in between comma separated values...

But then again, I'm not looking at the full code...

/J

On Wed, May 13, 2015 at 3:35 PM, Carlos Navarro Retamal <cnavarro at utalca.cl>
wrote:

> Hi Tsjerk
> Thanks for your reply.
> I found that the problem was the empty space between the number and the
> comma. How silly of me.
> Thanks in any case :)
> Carlos
> --
> Carlos Navarro Retamal
> Bioinformatics Engineering
> Ph. D (c) Applied Sciences.
> Center of Bioinformatics and Molecular Simulations. CBSM
> University of Talca
> Av. Lircay S/N, Talca, Chile
> T: (+56) 712201 798
> E: carlos.navarro87 at gmail.com or cnavarro at utalca.cl
>
>
>
> On May 13, 2015 at 3:28:52 PM, Tsjerk Wassenaar (tsjerkw at gmail.com<mailto:
> tsjerkw at gmail.com>) wrote:
>
> Hi Carlos,
>
> Use -box 20 20 10, without commas.
>
> Cheers,
>
> Tsjerk
> On May 13, 2015 2:25 PM, "João Henriques" <joao.henriques.32353 at gmail.com>
> wrote:
>
> > Dear Carlos,
> >
> > It's actually the other way around, it's trying to convert a string into
> a
> > float. I am absolutely not familiar with the code or the procedure, but
> > form a programming perspective, this is likely due to some input you're
> > providing that is not convertible to a float. For example, if you
> provide:
> > 'ABC123' as an argument to be internally converted to a float, it will
> fail
> > and raise an error such as yours.
> >
> > Maybe one of your inputs is required to be a 'number' and it's not.
> >
> > This as how far as I can go, being unfamiliar with Insane.py.
> >
> > Best regards,
> > João
> >
> > On Wed, May 13, 2015 at 12:03 PM, Carlos Navarro Retamal <
> > cnavarro at utalca.cl
> > > wrote:
> >
> > > Dear gmx users,
> > > I’m trying to create a thylakoid membrane (from cyanobacteria) with the
> > > following lipid composition:
> > > 18:1-16:0 PG 5.557%
> > > 16:1-16:0 PG 0.543%
> > > 18:1-16:0 DGDG 25.600%
> > > 18:1-16:0 MGDG 43.500%
> > > 18:1-16:0 SQDG 24.774%
> > > 16:0-16:0 SQDG 0.026%
> > > To do that, i’m using insane.py, by the following command line:
> > >
> > > ./insane.py -f PSII-CG.pdb -pbc square -box 20, 20, 10 -l CPG:0.5557 -l
> > > PPG:0.0543 -l CDGDG:2.56 -l CMGDG:4.35 -l CSQDB:2.4774 -l CSQDG:0.0026
> > -sol
> > > W -o system.gro
> > > But i’m getting the next error message:
> > > Traceback (most recent call last):
> > > File "./insane.py", line 559, in <module>
> > > options[ar].setvalue([args.pop(0) for i in range(options[ar].num)])
> > > File "./insane.py", line 441, in setvalue
> > > self.value = self.func(v[0])
> > > File "./insane.py", line 302, in readBox
> > > x = [ float(i) for i in a.split(",") ] + 6*[0]
> > > ValueError: could not convert string to float:
> > >
> > > Is this because i’m using float numbers to describe the specific amount
> > of
> > > lipids?
> > >
> > > If this is the case, can someone suggest me an approach to overcome
> this
> > > issue?
> > >
> > > Thanks in advance,
> > >
> > > Carlos
> > >
> > > --
> > > Carlos Navarro Retamal
> > > Bioinformatics Engineering
> > > Ph. D (c) Applied Sciences.
> > > Center of Bioinformatics and Molecular Simulations. CBSM
> > > University of Talca
> > > Av. Lircay S/N, Talca, Chile
> > > T: (+56) 712201 798
> > > E: carlos.navarro87 at gmail.com or cnavarro at utalca.cl
> > >
> > > --
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