[gmx-users] RE: gmx-users Digest, Vol 73, Issue 109

[Ricardo Cuya Guizado]

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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