[gmx-users] Insane.py problem

Wed May 13 18:32:27 CEST 2015

Hey :)

Right, I was confused. -box takes one argument, which is either a single
number for a cubic box, three comma separated values for a rectangular box
or nine comma separated values for a triclinic box. Note that the use of
-box causes the -pbc/-d options to be ignored.

Cheers,

Tsjerk
On May 13, 2015 17:30, "João Henriques" <joao.henriques.32353 at gmail.com>
wrote:

> I know it's a non issue now, but I was on my way home when I realized why
> it doesn't work with spaces.
> Since your values are being passed without quotes, the program interprets
> them as separate arguments due to the spaces. When splitting each one by
> the comma you get lists of two strings, one number string and one empty
> string. The empty string cannot be 'floated' and thus the error.
> On May 13, 2015 3:53 PM, "João Henriques" <joao.henriques.32353 at gmail.com>
> wrote:
>
> > If it works, it works, but for example:
> >
> > >>>a = '1,       1   ,      2   '
> > >>>[float(i) for i in a.split(',')]
> > [1.0, 1.0, 2.0]
> >
> > Best regards,
> > João
> >
> > On Wed, May 13, 2015 at 3:49 PM, Carlos Navarro Retamal <
> > cnavarro at utalca.cl> wrote:
> >
> >> 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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