[gmx-users] Insane.py problem

Carlos Navarro Retamal cnavarro at utalca.cl
Wed May 13 12:04:14 CEST 2015

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 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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