[gmx-users] Octahderal box

[David]

On Fri, 2005-09-09 at 21:25 +0100, Joanne Hanna wrote:
> Hi
> 
> I am having some difficulties with a truncated octahedron box.
> 
> I have made the box using:
> 
> editconf -f ENZ.pdb -d 1.0 -bt octahedron -o box.gro
> 
> viewing this in rasmol with the unitcell gives me what looks like a triclinic box.
> 
> After solvating this using:
> 
> genbox -cp box.gro -cs spc216.gro -o solv.gro
> 
> and viewing this in vmd i get what appears to be a cubic box with the enzyme not centered and sticking out of the solvated box.
> 
> Does anyone have any ideas where i am going wrong?
> 

try
trjconv -ur compact

> The output from the editconf is:
> 
> Read 5213 atoms
> Volume: 309.565 nm^3, corresponds to roughly 139300 electrons
> No velocities found
>     system size :  6.557  7.485  6.307 (nm)
>     diameter    :  7.941               (nm)
>     center      :  3.329 10.051  3.262 (nm)
>     box vectors :  6.557  7.485  6.307 (nm)
>     box angles  :  90.00  90.00  90.00 (degrees)
>     box volume  : 309.56               (nm^3)
>     shift       :  1.642 -3.022  0.796 (nm)
> new center      :  4.970  7.029  4.058 (nm)
> new box vectors :  9.941  9.941  9.941 (nm)
> new box angles  :  70.53 109.47  70.53 (degrees)
> new box volume  : 756.24               (nm^3)
> 
> gcq#231: "Let's Go Hang Out In a Mall" (LIVE)
> 
> and the bottom of the *.gro looks like:
> 
>   514PHE    HE1 5206   7.728   5.684   1.408
>   514PHE    CE2 5207   7.795   5.899   1.651
>   514PHE    HE2 5208   7.756   5.936   1.735
>   514PHE     CZ 5209   7.724   5.804   1.578
>   514PHE     HZ 5210   7.635   5.773   1.609
>   514PHE      C 5211   8.091   5.970   1.193
>   514PHE     O1 5212   7.983   5.994   1.114
>   514PHE     O2 5213   8.194   5.886   1.163
>    9.94094   9.37241   8.11675   0.00000   0.00000   3.31365   0.00000  -3.31365   4.68621
> 
> Any advice would be greatly appreciated.
> 
> Thanks
> 
> Jo
> 
> 
> 
> Joanne Hanna
> Department of Chemistry
> University of Warwick
> Coventry
> CV4 7AL
> 
> J.F.Hanna at warwick.ac.uk
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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