[EMAIL PROTECTED] 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.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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