[gmx-users] editconf/genbox problem in Gromacs 4.0

mldaniel at pnhs.purdue.edu mldaniel at pnhs.purdue.edu
Tue Oct 14 18:12:21 CEST 2008


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.

Matt Danielson

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