[gmx-users] octahedron box

[David van der Spoel]

On Fri, 2002-11-29 at 10:58, Barna Laszlo wrote:
> 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?
This is a FAQ, you want to run the pdb file through trjconv to get the
correct shape (-pbc and -ur options). mdrun does calculate with the
correct symmetry.


> 
> 
> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 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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