|
18 | 18 |
|
19 | 19 | amber94 Amber ff94 parameters for proteins and nucleic acids. |
20 | 20 | Note that N- and C-terminal amino acid charges differ |
21 | | - slightly from the authentic charge values. For these |
22 | | - terminal residues some charge is redistributed to or |
23 | | - from the alpha carbon atom; the total magnitude of the |
24 | | - redistribution is less than 0.01 e- in most cases. The |
25 | | - file reproduces the authentic ff94 energies. |
| 21 | + slightly from the authentic charge values;; note that |
| 22 | + N- and C-terminal amino acid charges differ slightly |
| 23 | + from the authentic charge values |
26 | 24 |
|
27 | 25 | amber96 Amber ff96 parameters for proteins and nucleic acids. |
28 | 26 | The only changes from Amber ff94 are in the phi/psi |
29 | | - torsional parameters. |
| 27 | + torsional parameters |
30 | 28 |
|
31 | 29 | amber98 Amber ff98 parameters for proteins and nucleic acids. |
32 | 30 | The only changes from Amber ff94 are in the glycosidic |
33 | | - torsional parameters. |
| 31 | + torsional parameters |
34 | 32 |
|
35 | 33 | amber99 Amber ff99 parameters for proteins and nucleic acids. |
36 | 34 | Uses the Cornell, et al (parm94) electrostatic model |
37 | 35 | but changes several geometric values from the above |
38 | | - Amber force fields. |
| 36 | + Amber force fields |
39 | 37 |
|
40 | | - amber99sb Amber ff99sb parameters for proteins and nucleic acids. |
41 | | - The only changes from Amber ff99 are to torsional |
| 38 | + amber99sb Amber ff99sb parameters for proteins and nucleic acids; |
| 39 | + the only changes from Amber ff99 are to torsional |
42 | 40 | parameters for phi/psi and phi'/psi', the latter being |
43 | | - the angles to the beta carbon atom. |
| 41 | + the angles to the beta carbon atom |
44 | 42 |
|
45 | 43 | amber14sb Amber ff14sb parameters for proteins as an improvement |
46 | 44 | on ff99sb, combined with OL15 DNA and OL3 RNA parameters |
47 | | - for nucleic acids, and TIP3P water parameters. |
| 45 | + for nucleic acids, and TIP3P water parameters; note that |
| 46 | + N- and C-terminal amino acid charges differ slightly |
| 47 | + from the authentic charge values |
48 | 48 |
|
49 | 49 | amber19sb Amber ff19sb parameters for proteins as an improvement |
50 | 50 | on ff14sb, combined with OL21 DNA and OL3 RNA parameters |
51 | | - for nucleic acids, and OPC water parameters. |
| 51 | + for nucleic acids, and OPC water parameters; note that |
| 52 | + N- and C-terminal amino acid charges differ slightly |
| 53 | + from the authentic charge values |
52 | 54 |
|
53 | 55 | amoeba AMOEBA force field for various small organic molecules |
54 | | - based on polarizable atomic multipole electrostatics. |
55 | | - Both 2004 (amoeba04) and 2009 (amoeba09) are provided. |
| 56 | + based on polarizable atomic multipole electrostatics; |
| 57 | + both 2004 (amoeba04) and 2009 (amoeba09) are provided |
56 | 58 |
|
57 | 59 | amoebabio Biopolymer parameters (protein and nucleic acid) for |
58 | | - the AMOEBA polarizable atomic multipole force field. |
59 | | - The 2009 and 2018 versions are provided. The -HFC23 |
| 60 | + the AMOEBA polarizable atomic multipole force field; |
| 61 | + the 2009 and 2018 versions are provided; the -HFC23 |
60 | 62 | modification of 2018 parameters from the Varma group |
61 | | - reworks many parameters involving ion interactions. |
| 63 | + reworks many parameters involving ion interactions |
62 | 64 |
|
63 | 65 | amoebail Ionic liquid parameters for the AMOEBA force field as |
64 | 66 | provided by Andres Cisneros at Univ. Texas at Dallas |
65 | 67 |
|
66 | 68 | amoebanuc Nucleic acid parameter for the AMOEBA polarizable atomic |
67 | | - multipole force field. The 2017 version is provided. |
| 69 | + multipole force field. The 2017 version is provided |
68 | 70 |
|
69 | 71 | amoebapro Protein parameters for the AMOEBA polarizable atomic |
70 | | - multipole force field. The original 2004 version and |
71 | | - current 2013 version are provided. |
| 72 | + multipole force field; the original 2004 version and |
| 73 | + current 2013 version are provided |
72 | 74 |
|
73 | 75 | basic A generic parameter file intended for simple and fast |
74 | 76 | geometry optimization of crude structures to avoid |
75 | | - steric clashes. The bond, angle and torsion parameters |
76 | | - are set to idealized values. The vdw values are loosely |
77 | | - based on OPLS, and electrostatics is largely neglected. |
| 77 | + steric clashes; the bond, angle and torsion parameters |
| 78 | + are set to idealized values; the vdw values are loosely |
| 79 | + based on OPLS, and electrostatics is largely neglected |
78 | 80 |
|
79 | | - charmm19 CHARMM19 parameters for proteins and water. The nucleic |
80 | | - acid values are not yet implemented. There are some |
| 81 | + charmm19 CHARMM19 parameters for proteins and water; the nucleic |
| 82 | + acid values are not yet implemented; there are some |
81 | 83 | differences between authentic CHARMM19 and the Tinker |
82 | 84 | version due to replacement of CHARMM impropers by |
83 | 85 | torsions for cases that involve atoms not bonded to |
84 | 86 | the trigonal atom and Tinker's use of all possible |
85 | 87 | torsions across a bond instead of a single torsion |
86 | | - per bond. |
| 88 | + per bond |
87 | 89 |
|
88 | | - charmm22 CHARMM22 parameters for proteins, plus heme and lipids. |
89 | | - Most of the nucleic acid and small model compound values |
| 90 | + charmm22 CHARMM22 parameters for proteins, plus heme and lipids; |
| 91 | + most of the nucleic acid and small model compound values |
90 | 92 | are not yet implemented. The file almost exactly |
91 | 93 | reproduces authentic CHARMM energies; there are small |
92 | 94 | differences are related to Tinker symmetrization of some |
93 | | - improper torsions. |
| 95 | + improper torsions |
94 | 96 |
|
95 | 97 | charmm27 CHARMM27 parameters for proteins, plus heme and lipids. |
96 | 98 | Identical to CHARMM22, except for addition of a CMAP |
97 | | - torsion-torsion phi-psi correction. Most nucleic acid and |
98 | | - model compound values are not implemented. There are small |
| 99 | + torsion-torsion phi-psi correction; most nucleic acid and |
| 100 | + model compound values are not implemented; there are small |
99 | 101 | changes from authentic CHARMM related to symmetrization of |
100 | | - some improper torsions, as well as in the CMAP correction. |
| 102 | + some improper torsions, as well as in the CMAP correction |
101 | 103 |
|
102 | | - charmm36 CHARMM36 parameters for proteins and nucleic acids. These |
| 104 | + charmm36 CHARMM36 parameters for proteins and nucleic acids; these |
103 | 105 | parameters include the CHARMM36m modifications intended |
104 | 106 | to provide a balanced model for folded and disordered |
105 | | - protein structures. |
| 107 | + protein structures |
106 | 108 |
|
107 | 109 | dang Polarizable force field parameters from Liem Dang at |
108 | | - Pacific Northwest National Laboratory. |
| 110 | + Pacific Northwest National Laboratory |
109 | 111 |
|
110 | 112 | hippo19 Preliminary parameters from 2019 for the HIPPO model |
111 | | - covering the monomer molecules in the S101 database. |
112 | | - These parameters are very preliminary, subject to |
113 | | - revision, and should not be used for production work. |
| 113 | + covering the monomer molecules in the S101 database; |
| 114 | + these parameters are very preliminary, subject to |
| 115 | + revision, and should not be used for production work |
114 | 116 |
|
115 | | - hoch Simple NMR-NOE force field of Hoch and Stern. |
| 117 | + hoch Simple NMR-NOE force field of Hoch and Stern |
116 | 118 |
|
117 | 119 | iwater Parameters for an AMOEBA-like polarizable multipole |
118 | 120 | model for water including only "direct" (non-iterative) |
119 | | - polarization. |
| 121 | + polarization |
120 | 122 |
|
121 | | - mm2 Full MM2(1991) parameters including pi-systems. The |
| 123 | + mm2 Full MM2(1991) parameters including pi-systems; the |
122 | 124 | anomeric and electronegativity correction terms are |
123 | | - not implemented. |
| 125 | + not implemented |
124 | 126 |
|
125 | 127 | mm3 Full MM3(2000) parameters including pi-systems. The |
126 | 128 | directional hydrogen bonding and electronegativity |
127 | 129 | bond length correction terms are implemented, but |
128 | 130 | the anomeric and Bohlmann correction terms are not |
129 | 131 | implemented. |
130 | 132 |
|
131 | | - mm3pro Protein-only version of the MM3 parameters. The |
| 133 | + mm3pro Protein-only version of the MM3 parameters; the |
132 | 134 | dielectric constant and some bond stretch and torsion |
133 | 135 | parameters are set to values recommended for high |
134 | | - dielectric and/or bulk environments. |
| 136 | + dielectric and/or bulk environments |
135 | 137 |
|
136 | 138 | mmff94 Full MMFF94 parameters for the Merck Molecular Force |
137 | | - Field. Validated against the data suite originally |
138 | | - deposited with the Computational Chemistry List (CCL). |
| 139 | + Field; validated against the data suite originally |
| 140 | + deposited with the Computational Chemistry List (CCL) |
139 | 141 |
|
140 | 142 | mmff94s A modified version of the MMFF94 parameters which exhibit |
141 | 143 | greater bias toward planarity at many types of trigonal |
142 | 144 | nitrogan such as amides, ureas, anilines, etc. |
143 | 145 |
|
144 | 146 | oplsaa08 OPLS-AA parameters from July 2008 with all-atom parameters |
145 | 147 | for proteins, nucleic acids and many general classes of |
146 | | - organic molecules. |
| 148 | + organic molecules |
147 | 149 |
|
148 | 150 | oplsaa24 OPLS-AA parameters based on results for a series of small |
149 | 151 | organic molecules generated by the LigParGen server, and |
150 | | - modified to provide transferable functional group values. |
| 152 | + modified to provide transferable functional group values |
151 | 153 |
|
152 | 154 | oplsaal A modified version of the 1997 OPLS-AA with optimized |
153 | 155 | torsional parameters for the protein backbone and side |
154 | | - chains as published in 2001. |
| 156 | + chains as published in 2001 |
155 | 157 |
|
156 | 158 | oplsua97 OPLS-UA containing united-atom parameters from 1997 for |
157 | | - proteins and many types of organic molecules. Explicit |
158 | | - hydrogens on polar atoms and aromatic carbons. |
| 159 | + proteins and many types of organic molecules; explicit |
| 160 | + hydrogens on polar atoms and aromatic carbons |
159 | 161 |
|
160 | 162 | smoothaa Parameters for use with the Tinker potential energy |
161 | 163 | smoothing methods. Based on the OPLS-AA parameters, but |
162 | | - with modifications to vdw and improper torsion terms. |
| 164 | + with modifications to vdw and improper torsion terms |
163 | 165 |
|
164 | | - smoothua Similar to SMOOTHAA, but based on OPLS-UA parameters. |
| 166 | + smoothua Similar to SMOOTHAA, but based on OPLS-UA parameters |
165 | 167 |
|
166 | 168 | uwater An AMOEBA-like water model, but having only a single |
167 | | - polarizable site centered on the oxygen atom. |
| 169 | + polarizable site centered on the oxygen atom |
168 | 170 |
|
169 | 171 | water03 The original 2003 AMOEBA water model parameters for a |
170 | | - polarizable multipole electrostatics model. |
| 172 | + polarizable multipole electrostatics model |
171 | 173 |
|
172 | 174 | water14 Parameters for a revision of the 2003 AMOEBA water model |
173 | 175 | fit to cluster data and a number of liquid properties |
174 | | - using the Force Balance optimization method. |
| 176 | + using the Force Balance optimization method |
175 | 177 |
|
176 | 178 | water21 Final HIPPO water parameters including charge flux terms, |
177 | | - as published in 2021. |
| 179 | + as published in 2021 |
178 | 180 |
|
179 | 181 | water22 An update of the AMOEBA 2003 water model derived by |
180 | | - Chengwen Liu at Univ. of Texas-Austin. Tuned parameters |
181 | | - are vdw and bond/angle constants, the model provides |
182 | | - good agreement with experiment and high-quality QM data. |
| 182 | + Chengwen Liu at Univ. of Texas-Austin; tunable parameters |
| 183 | + are vdw and bond/angle constants; the model provides |
| 184 | + good agreement with experiment and high-quality QM data |
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