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

[David van der Spoel]

mldaniel at pnhs.purdue.edu wrote:
> 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

It works for me. Is your input file empty?
Otherwise please file a bugzilla and upload the input file.

> 
> 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
> 
> 
> 
> 
> 
> 
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-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se