[gmx-users] related to box dimension : solvate protein-ligand complex
jalemkul at vt.edu
Mon Jun 4 14:00:16 CEST 2018
On 6/4/18 4:19 AM, Quyen V. Vu wrote:
> As i know that vmd cannot understand dodecahedron, he will take 3 numbers
> and plot a cubic while your box still is dodecahedron
VMD will display whatever coordinates it is given. GROMACS will, by
default, write coordinates using a triclinic representation of the unit
cell. One can "unwrap" the coordinates with trjconv, and in that case,
VMD will display exactly the unit cell shape that is defined, and it
certainly understands dodecahedral and octahedral shapes.
> On Fri, Jun 1, 2018, 06:48 Seketoulie Keretsu <sekekeretsu at gmail.com> wrote:
>> Dear All,
>> I am doing he Protein-ligand complex tutorial on gromacs 5.0.7 (newly
>> installed). I have successfully completed this tutorial earlier on
>> gromacs 4.6.
>> After the solvation step I found out that the protein-ligand complex
>> solvated system had a cubic shape while my box dimension (shown using
>> vmd command: pbc box) adopted a dodecahedron like shape. Please check
>> the attachment for details.
>> What could be the possible reason behind this? Kindly advise to
>> rectify the problem.
>> The was no error or warning uptill this.
>> Thank you.
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Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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