Dear Friends
I tried
to obtain the XY density maps of the heme using g_densmap tool.
The
molecule was centered in the box
The
system was rotated to maintain the XY plane on the molecular plane.
In the
reference gro file, the molecule was also centered and the plane XY was on the
molecular plane.
To create
the reference gro file
editconf_mpi_d
-f heme.gro -c -o heme_centered.gro -n index.ndx -princ
To center
the molecule in the box
trjconv_mpi_d
-f md10ns_heme.xtc -o md10ns_heme_centered.xtc -n index.ndx -s dmpr.tpr -center
-boxcenter rect -pbc atom
Rotations
and translations were eliminated and the XY axis on the XY molecular plane
trjconv_mpi_d
-f md10ns_heme_centered.xtc -o md10ns_heme_centrado_centered_rottrans.xtc -n
index.ndx -s heme_centered.gro -fit rot+trans
To obtain
the XY density map
g_densmap_d
-f md10ns_heme_centrado_centered_rottrans.xtc -s heme_centered.gro -n index.ndx
-o densmap.xpm
The
result show the molecule in the corner of the figure and a diffuse withe region
around the molecule.
I will expect a more defined region around the molecule and centered.
I need help, thanks
Regards
Ricardo
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