[gmx-users] octahedron box

[Barna Laszlo]

Hello!

I want to generate a dodecahedron box for simulating a protein in water, 
but I don't get correct shape.

I run the next script file:


#!/bin/bash

MOL=1ipdmonom

pdb2gmx -f ${MOL}.pdb -o ${MOL}hid.gro -p ${MOL}.top

editconf -f ${MOL}hid.gro -o ${MOL}edconf.gro  -bt dodecahedron -d 1.4

genbox -cp ${MOL}edconf.gro -cs -o ${MOL}_em.pdb -p ${MOL}.top

The last lines of 1ipdmonomedconf.gro are:

  345ALA     CA 5207   3.445   6.366   5.151
  345ALA     HA 5208   3.435   6.279   5.200
  345ALA     CB 5209   3.497   6.470   5.249
  345ALA    HB1 5210   3.431   6.482   5.324
  345ALA    HB2 5211   3.584   6.440   5.287
  345ALA    HB3 5212   3.509   6.557   5.202
  345ALA      C 5213   3.316   6.422   5.088
  345ALA     O1 5214   3.327   6.429   4.989
  345ALA     O2 5215   3.248   6.440   5.160
   9.78588   9.78588   6.91966   0.00000   0.00000   0.00000   0.00000   4.89294   4.89294


I checked the 1ipdmonom_em.pdb with rasmol and got a cubic shape.

What's the problem? 
Bed viewer or bed options?