[gmx-users] how to optimize the orientation of the protein in a dodecahedron

Thomas Evangelidis tevang3 at gmail.com
Thu Apr 26 13:18:13 CEST 2012

Dear GROMACS users,

I have noticed that for constant box dimensions the minimum distance from
the periodic images of a protein depends on the initial orientation of the
protein, whereas the orientation of the dodecahedron relative to the x,y,z
axes remains fixed. These are the command lines I use:

pdb2gmx_d4.5.5 -f protein.pdb -o protein.gro -p protein.top -ff
amber99sb-ildn -water tip3p -ignh
# set the new dodecahedron box dimensions
editconf_d4.5.5 -f protein.gro -bt dodecahedron -box 13 -o protein_box.gro
# solvate with TIP3P
genbox_d4.5.5 -cp protein_box.gro -cs spc216.gro -o protein_box_solv.gro -p
# add ions
grompp_d4.5.5 -f em_real.mdp -c protein_box_solv.gro -p protein.top -o
echo 13 | genion_d4.5.5 -s protein_ions.tpr -o protein_EM.gro -p
protein.top -pname NA -nname CL -np 3

grompp_d4.5.5 -f em_real.mdp -c protein_EM.gro -p protein.top -o
mpirun -np 2 mdrun_d4.5.5 -v -deffnm protein_EM

# to see a dodecahedron
echo 0 | trjconv_d4.5.5 -pbc mol -ur compact -f protein_EM.trr -s
protein_EM.tpr -o em_dodecahedron.xtc
# measure the minimum distance from the periodic images
echo 1 | g_mindist_d4.5.5 -f em_dodecahedron.xtc -s protein_EM.gro -pi

Is there any way to optimize the orientation of protein inside the
dodecahedron in order to get the maximum possible mindist?

Thanks in advance,



Thomas Evangelidis

PhD student

Biomedical Research Foundation, Academy of Athens

4 Soranou Ephessiou , 115 27 Athens, Greece

email: tevang at bioacademy.gr

          tevang3 at gmail.com

website: https://sites.google.com/site/thomasevangelidishomepage/
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