[gmx-users] Insane.py problem
Carlos Navarro Retamal
cnavarro at utalca.cl
Wed May 13 15:36:11 CEST 2015
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 Navarro Retamal
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:
Use -box 20 20 10, without commas.
On May 13, 2015 2:25 PM, "João Henriques" <joao.henriques.32353 at gmail.com>
> 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,
> 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
> > 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)
> > File "./insane.py", line 302, in readBox
> > x = [ float(i) for i in a.split(",") ] + 6*
> > ValueError: could not convert string to float:
> > Is this because i’m using float numbers to describe the specific amount
> > 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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