[gmx-users] octahedron box
David van der Spoel
spoel at xray.bmc.uu.se
Fri Nov 29 11:07:27 CET 2002
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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