[gmx-users] Octahderal box

[David]

On Sat, 2005-09-10 at 12:04 +0100, Joanne Hanna wrote:
> Hi
> 
> Thanks, this works. does this mean that i should now use the new *.gro file i have generated as the coordinates for water are quite different.
No it is identical for mdrun, which works with a triclinic
representation of the truncated octahedron. See manual.
> 
> Thanks for your help
> Jo
> 
> Joanne Hanna
> Department of Chemistry
> University of Warwick
> Coventry
> CV4 7AL
> 
> J.F.Hanna at warwick.ac.uk
> >>> spoel at xray.bmc.uu.se 09/10/05 07:46 AM >>>
> 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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