Hi Carlos, Use -box 20 20 10, without commas.
Cheers, Tsjerk On May 13, 2015 2:25 PM, "João Henriques" <joao.henriques.32...@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 < > cnava...@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.navarr...@gmail.com or cnava...@utalca.cl > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.