6
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Given a pdb file that looks like the following:

TITLE     Generated by gmx solvate
REMARK    THIS IS A SIMULATION BOX
CRYST1   12.500   12.500   12.500  90.00  90.00  90.00 P 1           1
MODEL        1
ATOM      1  OW  SOL     3       5.300  10.220   4.860  1.00  0.00
ATOM      2  HW1 SOL     3       6.200   9.970   4.700  1.00  0.00
ATOM      3  HW2 SOL     3       5.260  11.150   4.630  1.00  0.00
ATOM      5  OW  SOL     4       8.140   4.780   4.990  1.00  0.00
ATOM      6  HW1 SOL     4       7.890   5.660   5.270  1.00  0.00
ATOM      7  HW2 SOL     4       8.110   4.810   4.030  1.00  0.00
ATOM      9  OW  SOL     5       2.560   5.060   4.270  1.00  0.00
ATOM     10  HW1 SOL     5       2.880   5.940   4.090  1.00  0.00
ATOM     11  HW2 SOL     5       2.440   5.040   5.220  1.00  0.00
ATOM     13  OW  SOL     6       3.340   9.190  13.280  1.00  0.00
ATOM     14  HW1 SOL     6       3.970   8.660  12.790  1.00  0.00
ATOM     15  HW2 SOL     6       3.150   9.930  12.710  1.00  0.00
ATOM     17  OW  SOL     7       6.550   2.610   5.140  1.00  0.00
ATOM     18  HW1 SOL     7       7.130   3.370   5.160  1.00  0.00
ATOM     19  HW2 SOL     7       5.900   2.820   4.470  1.00  0.00

I want to calculate and plot the electric field/electrostatic forces of this configuration. I have tried a few things like g_elpot but to no affect. Is there a tried and tested method anybody else has ?

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  • $\begingroup$ +1 but which columns of this file do you want to plot? $\endgroup$ Feb 26, 2022 at 14:58
  • $\begingroup$ @NikeDattani none from this file. My expectation is that a force-field will calculate the charges on atoms in this file and some md engine will calculate the electrostatic forces - which i would then like to plot to see the direction of electric field at different atoms $\endgroup$
    – fireball.1
    Feb 26, 2022 at 17:55
  • $\begingroup$ Do you mean the dipole moment? $\endgroup$
    – S R Maiti
    Feb 26, 2022 at 18:15
  • $\begingroup$ @SRMaiti I suppose that should work too. $\endgroup$
    – fireball.1
    Feb 27, 2022 at 15:03
  • $\begingroup$ You can try to use this PDB as input to run a molecular dynamic job. Then use the resulting file (that should have the charges from the forcefield) and plot the Electrostatic Potential Surface using software like Jmol, MAESTRO, CHIMERA, etc. All of them will use the charges from the PDB file. I think CHIMERA can associate charges and do al the work. About plotting the electrostatic forces, these forces are two-particle forces, so, you can use the Coulomb law to calculate the force between one atom and all the other ones. $\endgroup$
    – Camps
    Feb 28, 2022 at 12:43

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