Hey Alan, I think there is a litle bug in editconf. If you add a CRYST1 line with some random numbers into the first Complex.pdb, editconf works fine adds the corret CRYST1 line according to your option (-d and -bt).
Best, Jochen Alan wrote: > Hello, > So this command used to work fine: > > editconf -bt triclinic -f Complex.pdb -o Complex.pdb -d 1.0 > > Now, with gmx 4.0 (from fink for Mac Intel Leopard), I got a warning: > > WARNING: No boxtype specified - distance condition applied in each > dimension. > > (no box information is inserted in the pdb file as it used to do in gmx 3) > > and then when I try: > > genbox -cp Complex.pdb -cs ffamber_tip3p.gro -o Complex_b4ion.pdb -p > Complex.top > > I get this error: > > ------------------------------------------------------- > Program genbox, VERSION 4.0 > Source code file: gmx_genbox.c, line: 744 > > Fatal error: > Undefined solute box. > Create one with editconf or give explicit -box command line option > ------------------------------------------------------- > > If I change '-o Complex.pdb' to '-o Complex.gro' and so on (i.e, if I use > gro instead of pdb), all work fine. > > So, pdb format is not ok anymore with gmx commands or there's a bug here? > > Many thanks in advance, > Alan > > > ------------------------------------------------------------------------ > > _______________________________________________ > 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 -- ************************************************ Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ************************************************ _______________________________________________ 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