How to make electrostatic potential map
Therefore, I ll show you the easy method " copy and paste "
①Change the name of file name created by gaussan
**cubename**.cub → **cubename**.cube
②open "**cubename**.cube" by using textedit
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Title Card Required potential=scf
Electrostatic potential from Total SCF Density
94 -18.366598 -13.153513 -13.708625 1 ←delete "1" and then save
111 0.333333 0.000000 0.000000
87 0.000000 0.333333 0.000000
83 0.000000 0.000000 0.333333
6 6.000000 -0.000028 3.242997 -0.000312
1 1.000000 0.000027 5.286605 -0.000593
6 6.000000 -2.305309 1.928239 -0.057792
6 6.000000 -2.329696 -0.735406 -0.082642
6 6.000000 -0.000123 -1.988648 0.000363
1 1.000000 -0.000163 -4.041196 0.000610
6 6.000000 2.329505 -0.735480 0.083050
6 6.000000 2.305205 1.928152 0.057516
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③Put these two files, on desk top
**cubename**.cube
●●●model name●●●.pdb
④copy the text below and paste on the command line of Pymol
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cd ~/desktop
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load **cubename**.cube
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load ●●●model name●●●.pdb
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isosurface A, **cubename**, 0.2
(you can change olenge number such as 0.3 )
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ramp_new ESPM, **cubename**, [0.19,0.19999934595, 0.1999994595, 0.1999995, 0.21], [red,orange, yellow,green, blue]
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set surface_ramp_above_mode
set surface_color, ESPM
you have to change the numbers. acrually it is difficult to fix it.
[0.19,0.19999934595, 0.1999994595, 0.1999995, 0.21],
ramp_new ESPM, **cubename**, [0.19,0.19999934595, 0.1999994595, 0.1999995, 0.21], [red,orange, yellow,green, blue]
set surface_color, ESPM
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this is magic word to change.
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