[gmx-users] gbsa.itp for amber ff

[Yun Shi]

Hi all,

If I want do MD simulation with amber ff and implicit solvent, would
including gbsa.itp in .top file and specifying parameters in .mdp as
follows be sufficient?

implicit_solvent = GBSA
gb_algorithm     = OBC
nstgbradii	 = 1.0
rgbradii         = 1.0
gb_epsilon_solvent = 78.3
gb_dielectric_offset = 0.009
sa_algorithm         = Ace-approximation
sa_surface_tension   = 0.0054


But I wonder if this line is problematic in gbsa.itp: ";Br
0.1      1      1        0.125     0.85 ; H". Is this for a bromine
atom or hydrogen?

[ implicit_genborn_params ]

; atype      sar      st     pi       gbr	hct
;Br           0.1      1      1        0.125     0.85 ; H
C            0.172    1      1.554    0.1875    0.72 ; C
CA           0.18     1      1.037    0.1875    0.72 ; C
....


Regards,
Yun