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ff_Mg_tip4pd.itp
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ff_Mg_tip4pd.itp
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; **************************************************************************************************
; * Title of publication: "Systematic Optimization of Mg2+ Force Fields for Biomolecular *
; * Simulations with Accurate Solvation, Ion-pairing, and Water Exchange Properties *
; * in SPC/E, TIP3P-fb, TIP4P/2005, TIP4P-Ew, and TIP4P-D" *
; * Authors: Kara K. Grotz and Nadine Schwierz *
; * For implementation please cite: K. K. Grotz, N. Schwierz (tba) *
; * doi: tba *
; * *
; * Note 1: This force field for Magnesium was optimized with the >>>TIP4P-D<<< water model (doi:10.1021/jp508971m) *
; * Note 2: Lorentz-Berthelot combination rules required *
; * Note 3: This force field was optimized to be used with Cl parameters that are optimized in the same publication *
; * Note 4: This force field was optimized to be used with paramBSC0chiOL3 parameters for RNA (amber14.ff)
; * *
; * CXY - Cl parameters *
; * mMg - MG with water exchange as in experiment *
; * nMg - MG with accellerated water exchange *
; * *
; **************************************************************************************************
[ atomtypes ]
; name at.num mass charge ptype sigma epsilon
mMg 12 24.305 2 A 0.096035 621.504072
nMg 12 24.305 2 A 0.097035 680.009868
CXY 17 35.45 -1 A 0.509112 0.035496
; all atoms from the RNA (these parameters have just been copied from paramBSC0chiOL3 for RNA (amber14.ff))
C 6 12.01 0.0000 A 3.39967e-01 3.59824e-01
CA 6 12.01 0.0000 A 3.39967e-01 3.59824e-01
CB 6 12.01 0.0000 A 3.39967e-01 3.59824e-01
CI 6 12.01 0.0000 A 3.39967e-01 4.57730e-01
CP 6 12.01 0.0000 A 3.39967e-01 3.59824e-01
CQ 6 12.01 0.0000 A 3.39967e-01 3.59824e-01
CS 6 12.01 0.0000 A 3.39967e-01 3.59824e-01
CT 6 12.01 0.0000 A 3.39967e-01 4.57730e-01
C4 6 12.01 0.0000 A 3.39967e-01 3.59824e-01
C5 6 12.01 0.0000 A 3.39967e-01 3.59824e-01
H 1 1.008 0.0000 A 1.06908e-01 6.56888e-02
HO 1 1.008 0.0000 A 0.00000e+00 0.00000e+00
H1 1 1.008 0.0000 A 2.47135e-01 6.56888e-02
H2 1 1.008 0.0000 A 2.29317e-01 6.56888e-02
HA 1 1.008 0.0000 A 2.59964e-01 6.27600e-02
H4 1 1.008 0.0000 A 2.51055e-01 6.27600e-02
H5 1 1.008 0.0000 A 2.42146e-01 6.27600e-02
NA 7 14.01 0.0000 A 3.25000e-01 7.11280e-01
NB 7 14.01 0.0000 A 3.25000e-01 7.11280e-01
NC 7 14.01 0.0000 A 3.25000e-01 7.11280e-01
N2 7 14.01 0.0000 A 3.25000e-01 7.11280e-01
N* 7 14.01 0.0000 A 3.25000e-01 7.11280e-01
O 8 16.00 0.0000 A 2.95992e-01 8.78640e-01
O2 8 16.00 0.0000 A 2.95992e-01 8.78640e-01
OH 8 16.00 0.0000 A 3.06647e-01 8.80314e-01
OS 8 16.00 0.0000 A 3.00001e-01 7.11280e-01
P 15 30.97 0.0000 A 3.74177e-01 8.36800e-01
[ nonbond_params ]
; i j func sigma epsilon
mMg mMg 1.000 0.096035 621.504072
mMg CXY 1.000 0.481091 0.469690
mMg C 1.000 0.2889603255 4.88109435372
mMg CA 1.000 0.2889603255 4.88109435372
mMg CB 1.000 0.2889603255 4.88109435372
mMg CI 1.000 0.2889603255 5.50524724152
mMg CP 1.000 0.2889603255 4.88109435372
mMg CQ 1.000 0.2889603255 4.88109435372
mMg CS 1.000 0.2889603255 4.88109435372
mMg CT 1.000 0.2889603255 5.50524724152
mMg C4 1.000 0.2889603255 4.88109435372
mMg C5 1.000 0.2889603255 4.88109435372
mMg H 1.000 0.13450047325 2.08553654022
mMg HO 1.000 0.06364719625 0.0
mMg H1 1.000 0.2274359175 2.08553654022
mMg H2 1.000 0.215627038 2.08553654022
mMg HA 1.000 0.23593833725 2.03851356969
mMg H4 1.000 0.2300338975 2.03851356969
mMg H5 1.000 0.22412945775 2.03851356969
mMg NA 1.000 0.27904094625 6.86265928801
mMg NB 1.000 0.27904094625 6.86265928801
mMg NC 1.000 0.27904094625 6.86265928801
mMg N2 1.000 0.27904094625 6.86265928801
mMg N* 1.000 0.27904094625 6.86265928801
mMg O 1.000 0.25981589425 7.62741935607
mMg O2 1.000 0.25981589425 7.62741935607
mMg OH 1.000 0.2668774955 7.63468184366
mMg OS 1.000 0.262472859 6.86265928801
mMg P 1.000 0.311633003 7.443599106
nMg nMg 1.000 0.097035 680.009868
nMg CXY 1.000 0.481886 0.491300
nMg C 1.000 0.2453984731 4.43304884946
nMg CA 1.000 0.2453984731 4.43304884946
nMg CB 1.000 0.2453984731 4.43304884946
nMg CI 1.000 0.2453984731 4.99990948371
nMg CP 1.000 0.2453984731 4.43304884946
nMg CQ 1.000 0.2453984731 4.43304884946
nMg CS 1.000 0.2453984731 4.43304884946
nMg CT 1.000 0.2453984731 4.99990948371
nMg C4 1.000 0.2453984731 4.43304884946
nMg C5 1.000 0.2453984731 4.43304884946
nMg H 1.000 0.11452419165 1.89410093109
nMg HO 1.000 0.05449000425 0.0
nMg H1 1.000 0.1932686635 1.89410093109
nMg H2 1.000 0.1832629656 1.89410093109
nMg HA 1.000 0.20047278845 1.85139429396
nMg H4 1.000 0.1954699395 1.85139429396
nMg H5 1.000 0.19046709055 1.85139429396
nMg NA 1.000 0.23699375425 6.23272193822
nMg NB 1.000 0.23699375425 6.23272193822
nMg NC 1.000 0.23699375425 6.23272193822
nMg N2 1.000 0.23699375425 6.23272193822
nMg N* 1.000 0.23699375425 6.23272193822
nMg O 1.000 0.22070431185 6.92728313581
nMg O2 1.000 0.22070431185 6.92728313581
nMg OH 1.000 0.2266876271 6.93387898501
nMg OS 1.000 0.2229555658 6.23272193822
nMg P 1.000 0.2646090986 6.76033611757