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ff_Mg.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" *
; * Authors: Kara K. Grotz and Sergio Cruz-Leon and Nadine Schwierz *
; * For implementation please cite: K. K. Grotz, S. Cruz-Leon, N. Schwierz (JCTC, 2021, https://pubs.acs.org/doi/10.1021/acs.jctc.0c01281) *
; * doi: 10.1021/acs.jctc.0c01281 *
; * *
; * Note 1: This force field for Magnesium was optimized with the TIP3P water model *
; * Note 2: Lorentz-Berthelot combination rules required *
; * Note 3: This force field was optimized to be used with Cl parameters of Mamatkulov-Schwierz (doi:10.1063/1.5017694) *
; * Note 4: This force field was optimized to be used with paramBSC0chiOL3 parameters for RNA (amber14.ff)
; * *
; * CXY - Cl (Mamatkulov-Schwierz) *
; * 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 0.101934 235.804213166223
nMg 12 24.305 2 A 0.102534 389.798801356
; Chloride parameters from Mamatkulov-Schwierz (doi:10.1063/1.5017694)
CXY 17 35.45 -1 A 0.440939 0.283829
; 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
CXY CXY 1.000 0.440939 0.283829
mMg mMg 1.000 0.101934 235.804213166
mMg CXY 1.000 0.48782511 0.8180958
mMg C 1.000 0.25133119375 2.94761543562
mMg CA 1.000 0.25133119375 2.94761543562
mMg CB 1.000 0.25133119375 2.94761543562
mMg CI 1.000 0.25133119375 3.32453146161
mMg CP 1.000 0.25133119375 2.94761543562
mMg CQ 1.000 0.25133119375 2.94761543562
mMg CS 1.000 0.25133119375 2.94761543562
mMg CT 1.000 0.25133119375 3.32453146161
mMg C4 1.000 0.25133119375 2.94761543562
mMg C5 1.000 0.25133119375 2.94761543562
mMg H 1.000 0.1187788875 1.25942242703
mMg HO 1.000 0.0579749625 0.0
mMg H1 1.000 0.19853299375 1.25942242703
mMg H2 1.000 0.18839900625 1.25942242703
mMg HA 1.000 0.2058294875 1.2310260012
mMg H4 1.000 0.20076249375 1.2310260012
mMg H5 1.000 0.1956955 1.2310260012
mMg NA 1.000 0.2428187125 4.14425105946
mMg NB 1.000 0.2428187125 4.14425105946
mMg NC 1.000 0.2428187125 4.14425105946
mMg N2 1.000 0.2428187125 4.14425105946
mMg N* 1.000 0.2428187125 4.14425105946
mMg O 1.000 0.2263204125 4.60607753071
mMg O2 1.000 0.2263204125 4.60607753071
mMg OH 1.000 0.23238044375 4.61046323173
mMg OS 1.000 0.22860053125 4.14425105946
mMg P 1.000 0.27078813125 4.49507139822
nMg nMg 1.000 0.102534 389.798801356
nMg CXY 1.000 0.4883651 1.0518375
nMg C 1.000 0.25299994675 2.9607744331
nMg CA 1.000 0.25299994675 2.9607744331
nMg CB 1.000 0.25299994675 2.9607744331
nMg CI 1.000 0.25299994675 3.33937311992
nMg CP 1.000 0.25299994675 2.9607744331
nMg CQ 1.000 0.25299994675 2.9607744331
nMg CS 1.000 0.25299994675 2.9607744331
nMg CT 1.000 0.25299994675 3.33937311992
nMg C4 1.000 0.25299994675 2.9607744331
nMg C5 1.000 0.25299994675 2.9607744331
nMg H 1.000 0.1197484635 1.26504484858
nMg HO 1.000 0.0586238145 0.0
nMg H1 1.000 0.19992325075 1.26504484858
nMg H2 1.000 0.18973580925 1.26504484858
nMg HA 1.000 0.2072582315 1.23652165299
nMg H4 1.000 0.20216451075 1.23652165299
nMg H5 1.000 0.19707079 1.23652165299
nMg NA 1.000 0.2444425645 4.16275218026
nMg NB 1.000 0.2444425645 4.16275218026
nMg NC 1.000 0.2444425645 4.16275218026
nMg N2 1.000 0.2444425645 4.16275218026
nMg N* 1.000 0.2444425645 4.16275218026
nMg O 1.000 0.2278572405 4.62664037682
nMg O2 1.000 0.2278572405 4.62664037682
nMg OH 1.000 0.23394923675 4.63104565687
nMg OS 1.000 0.23014938625 4.16275218026
nMg P 1.000 0.27255951425 4.51513868125