Please keep correspondence on the list. If you want to post images, do so via
the web so that everyone can have a look.
Andrew Voronkov wrote:
Dear Justin,
I am very sorry for writing to you directly, but seems like gmx user list
doesn't like attachments. I have problems with editconf command line.
I've used the command lines:
editconf -c –f conf.gro –bt dodecahedron –d 0.5 –o box.gro - to get
dodecahedron and to center the protein, then I've used:
genbox –cp box.gro –cs spc216.gro –p topol.top –o solvated.gro
But
1) I get a cubic box, not dodecahedron
This is a VMD issue, not a Gromacs problem. By default, VMD will display
rectangular or triclinic boxes based on what it finds in the .gro file.
Use trjconv -pbc mol -ur compact to get a "correct" representation.
2) protein is not in the center of the box, but in the edge (see attachemnt
screenshot).
I've checked the flags -looks like they're ok, but seems like editconf doesn't see
-c flag and dodecahedron parameter.
Again, just a VMD thing.
The initial conf.gro and topol.top are also attached.
These are not useful for diagnosis; the screenshot is enough.
-Justin
Best regards,
Andrew
------------------------------------------------------------------------
--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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