[gmx-users] Protonated ligand free energy calculation in water

[Rolly Ng]

Dear GROMACS users,

 

I read and followed Dr. Lemkul's tutorial on Free Energy Calculation on the
webpage, http://www.mdtutorials.com/gmx/free_energy/index.html

 

It is very helpful and easy to follow, but my ligand is protonated so the
atomic charges in the topol.top are non-zero.

 

The above tutorial also indicates that Coulombic interactions can be
applied, but I would like to know how it can be done?

 

    vdw_lambdas             = 0.00 0.05 0.10 ... 1.00 1.00 1.00 ... 1.00

    coul_lambdas            = 0.00 0.00 0.00 ... 0.00 0.05 0.10 ... 1.00

 

Here is the [ atoms ] in my topol.top and your advise is highly appreciated!


 

[ atoms ]

;   nr       type  resnr residue  atom   cgnr    charge       mass  typeB
chargeB      massB

; residue    1 MT3 rtp MT3 q 2.0

    1         nh      1    MT3     N1      1 -0.83505600  14.010000   ; qtot
-0.835056

    2         cz      1    MT3     C1      2 0.85138300  12.010000   ; qtot
0.016327

    3         nh      1    MT3     N2      3 -0.51848300  14.010000   ; qtot
-0.502156

    4         nh      1    MT3     N3      4 -0.83505600  14.010000   ; qtot
-1.337212

    5         c3      1    MT3     C2      5 -0.34660600  12.010000   ; qtot
-1.683818

    6         nh      1    MT3     N4      6 0.02468700  14.010000   ; qtot
-1.659131

    7         nh      1    MT3     N5      7 -0.80566500  14.010000   ; qtot
-2.464796

    8         cz      1    MT3     C3      8 0.57808800  12.010000   ; qtot
-1.886708

    9         c3      1    MT3     C4      9 -0.34660600  12.010000   ; qtot
-2.233314

   10         hn      1    MT3     H1     10 0.47045200   1.008000   ; qtot
-1.762862

   11         hn      1    MT3     H2     11 0.47045200   1.008000   ; qtot
-1.292410

   12         hn      1    MT3     H3     12 0.38772400   1.008000   ; qtot
-0.904686

   13         hn      1    MT3     H4     13 0.47045200   1.008000   ; qtot
-0.434234

   14         h1      1    MT3     H5     14 0.17432200   1.008000   ; qtot
-0.259912

   15         h1      1    MT3     H6     15 0.17432200   1.008000   ; qtot
-0.085590

   16         h1      1    MT3     H7     16 0.17432200   1.008000   ; qtot
0.088732

   17         hn      1    MT3     H8     17 0.45892600   1.008000   ; qtot
0.547658

   18         h1      1    MT3     H9     18 0.17432200   1.008000   ; qtot
0.721980

   19         h1      1    MT3    H10     19 0.17432200   1.008000   ; qtot
0.896302

   20         h1      1    MT3    H11     20 0.17432200   1.008000   ; qtot
1.070624

   21         hn      1    MT3    H12     21 0.45892600   1.008000   ; qtot
1.529550

   22         hn      1    MT3    H13     22 0.47045200   1.008000   ; qtot
2.000002

 

Thank you,

Rolly