Hi Alessandro, editconf encounters a bad box in the input file and I think it first replaces that with a standard box internally. Check the box at the end of box.gro to see if the result is what it should be (nine numbers, according to the specification of the rhombic dodecahedon in Chapter 3 of the manual).
Cheers, Tsjerk On 11/10/08, Alessandro Casoni <[EMAIL PROTECTED]> wrote: > Hi all, > when i use "editconf" to generate a dodecahedron box with the command: > > editconf -f protein.gro -bt dodecahedron -o box.gro -d 0.9 > > the output show me the following message: > > ..... > WARNING 1 [file aminoacids.dat, line 1]: > Bad box in file protein.gro > > Generated a cubic box 6.941 x 4.939 x 7.460 > ..... > > what is the mean of "bad box in file"? > and why editconf generates a cubic box? > > I use gromacs 4.0 > regards, > Alessandro > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [EMAIL PROTECTED] > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
