Users, I have recently upgraded from Gromacs3.3 to Gromacs4.0 and I seem to be encountering a problem when trying to solvate a protein in a water box.
Editconf command: editconf -bt octahedron -f prot2.pdb -o prot2_test.pdb -c -d 1.0 The output from editconf appears to be normal and the problem doesn't arise until i issue the genbox command: genbox -cp prot2_test.pdb -cs spc216.gro -o prot_4ion.pdb -p prot.top Error message that follows: ------------------------------------------------------- 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 ------------------------------------------------------- On another machine running version 3.3 i have issued the same commands and there is no error message. When examining the difference between the prot2_test.pdb files, version 4.0 seems to be leaving out the line containing coordinate information about the water box. Line missing @ the top of the prot2_test.pdb in version 4.0: CRYST1 96.102 96.102 96.102 70.53 109.47 70.53 P 1 1 Has anyone else experienced this problem? Are there any flags that i am missing that i now need to specify? Any information would be appreciated. Thanks, Matt Danielson _______________________________________________ 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
