Ah okey, Thank you! > > > On 7/3/12 5:10 AM, [email protected] wrote: >> Hi everybody, >> I want to put my protein in the box with editconf but when I look at it >> it >> is always at the border of the box and not at the center. I tried it >> with >> those two commands: >> >> editconf -f 3m71.gro -o 3m71_box.gro -center 4.59340 4.59470 5.17330 >> -c -bt dodecahedron -d 1.0 2>>logErr 1>>logOut >> >> editconf -f 3m71.gro -o 3m71_box.gro -c -bt dodecahedron -d 1.0 >> 2>>logErr >> 1>>logOut >> >> With the first command it is at the upper border and with the second >> command it is at the right border. The coordinates of the firs command >> are >> from the 3m71.gro file. >> >> Can you please tell me what is wrong? >> > > Nothing. When visualizing the unit cell, it will appear as a triclinic > box with > the protein in a seemingly random location. You can re-wrap the unit cell > with > trjconv -pbc mol -ur compact (which requires a .tpr file) to see the > dodecahedral unit cell with everything placed as you would expect. > > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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