MacroModel Reference Manual - ISP

More documents

Recommendations

Info

Appendix G: MINTA BackgroundCarlson, H. A.; Jorgensen, W. L. J. Phys. Chem. 1995, 99, 10667.DesJarlais, R. L.; Sheridan, R. P.; Seibel, G. L.; Dixon, J. S.; Kuntz, I. D.; Venkataraghavan, R.J. Med. Chem. 1988, 31, 722.DeWitte, R. S.; Shakhnovich, E. I. J. Am. Chem. Soc. 1996, 118, 11733.Essex, J. W.; Severance, D. L.; Jorgensen, W. L. J. Phys. Chem. B 1997, 101, 9663.Gilson, M. K.; Given, J. A.; Bush, B. L.; McCammon, J. A. Biophys. 1997, J. 72, 1047.Goodsell, D. S.; Olson, A. J. Proteins 1990, 8, 195.Guida, W. C.; Bohacek, R. S.; Erion, M. D. J. Comput. Chem. 1992, 13, 214.Head, M. S.; Given, J. A.; Gilson, M. K. J. Phys. Chem. A 1997, 101, 1609.Hermans, J.; Wang, L. J. Am. Chem. Soc. 1997, 119, 2707.Hultén, J.; Bonham, N. M.; Nillroth, U.; Hansson, T.; Zuccarello, G.; Bouzide, A.; Åqvist, J.;Classon, B.; Danielson, U. H.; Karlén, A.; Kvarnström, I.; Samuelsson, B.; Hallberg, A. J.Med. Chem. 1997, 40, 885.Jones-Hertzog, D. K.; Jorgensen, W. L. J. Med. Chem. 1997, 40, 1539.Jorgensen, W. L. Acc. Chem. Res. 1989, 22, 184.Keser, G. M.; Kolossváry, I.; Bertók, B. J. Am. Chem. Soc. 1997, 119, 5126.Kollman, P. A. Chem. Rev. 1993, 93, 2395.Kollman, P. A. Acc. Chem. Res. 1996, 29, 461.Lamb, M. L.; Jorgensen, W. L. Curr. Op. Chem. Biol. 1997, 1, 449.McCammon, J. A.; Harvey, S. C. Dynamics of Proteins and Nucleic Acids; Cambridge UniversityPress; Cambridge, 1987.McDonald, N. A.; Carlson, H. A.; Jorgensen W. L. J. Phys. Org. Chem. 1997, 10, 563.McMartin, C.; Bohacek, R. S. J. Comput.-Aided Mol. Design 1995, 9, 237.McMartin, C.; Bohacek, R. S. J. Comput.-Aided Mol. Design 1997, 11, 333.Metropolis, N.; Rosenbluth, A. W.; Rosenbluth, M. N.; Teller, A.; Teller E. J. Chem. Phys.1953, 21, 1087.Morris, G. M.; Goodsell, D. S.; Huey, R.; Olson, A. J. J. Comput.-Aided Mol. Design 1996, 10,293.234MacroModel 9.7 Reference Manual
Appendix G: MINTA BackgroundPaulsen, M. D.; Ornstein, R. L. Protein Engng. 1996, 9, 567.Qiu, D.; Shenkin, P. S.; Hollinger, F. P.; Still, W. C. J. Phys. Chem. A 1997, 101, 3005.Roux, B.; Yu, H.-A.; Karplus, M. J. Phys. Chem. 1990, 94, 4683.Senderowitz, H.; Guarnieri, F.; Still, W. C. J. Am. Chem. Soc. 1995, 117, 8211.Senderowitz, H.; McDonald, D. Q.; Still, W. C. J. Org. Chem. 1997, 62, 9123.Shenkin, P. S.; Farid, H.; Fetrow J. S. Proteins: Struct., Funct., Genet. 1996, 26, 323.Simonson, T.; Archontis, G.; Karplus, M. J. Phys. Chem. B 1997, 101, 8349.Still, W. C.; Tempczyk, A.; Hawley, R. C.; Hendrickson, T. J. Am. Chem. Soc. 1990, 112, 6127.Straatsma, T. P.; McCammon, J. A. Ann. Rev. Phys. Chem. 1992, 43, 407.Van Gunsteren, W. F.; Mark, A. E. Eur. J. Biochem. 1992, 204, 947.Warshel, A.; Russell, S. T. Q. Rev. Biophys. 1984, 17, 283.Welch, W.; Ruppert, J.; Ajay, N. J. Chem. Biol. 1996, 3, 449.Zwanzig, R. W. J. Chem. Phys. 1954, 22, 1420.MacroModel 9.7 Reference Manual 235
Page 1 and 2:
MacroModel Reference ManualMacroMod
Page 3 and 4:
ContentsDocument Conventions ......
Page 5 and 6:
ContentsChapter 5: MINTA...........
Page 7 and 8:
Document ConventionsIn addition to
Page 9 and 10:
MacroModel Reference ManualChapter
Page 11 and 12:
Chapter 1: Capabilities and New Fea
Page 13 and 14:
Page 15 and 16:
Page 17 and 18:
Page 19 and 20:
Page 21 and 22:
Chapter 2: Running MacroModelTable
Page 23 and 24:
Chapter 2: Running MacroModelstruct
Page 25 and 26:
Chapter 2: Running MacroModel2.2 Jo
Page 27 and 28:
Chapter 2: Running MacroModelfile
Page 29 and 30:
Chapter 2: Running MacroModelusing
Page 31 and 32:
Chapter 2: Running MacroModel2.3.3.
Page 33 and 34:
Chapter 2: Running MacroModelalso s
Page 35 and 36:
Page 37 and 38:
Chapter 3: Running MacroModel with
Page 39 and 40:
Page 41 and 42:
Chapter 4: Operation Codesarg1Frequ
Page 43 and 44:
Chapter 4: Operation Codesarg3Hydro
Page 45 and 46:
Chapter 4: Operation CodesTable 4.1
Page 47 and 48:
Chapter 4: Operation CodesLimitatio
Page 49 and 50:
Chapter 4: Operation Codesarg3Note:
Page 51 and 52:
Chapter 4: Operation Codes2 Use for
Page 53 and 54:
Chapter 4: Operation Codes1 The cur
Page 55 and 56:
Chapter 4: Operation Codes1 Use fas
Page 57 and 58:
Chapter 4: Operation Codesway on th
Page 59 and 60:
Chapter 4: Operation Codes
Page 61 and 62:
Chapter 4: Operation CodesIf solvat
Page 63 and 64:
Chapter 4: Operation CodesFMNR has
Page 65 and 66:
Chapter 4: Operation Codesarg1Listi
Page 67 and 68:
Chapter 4: Operation Codesnarg3For
Page 69 and 70:
Chapter 4: Operation Codesarg3 Symm
Page 71 and 72:
Chapter 4: Operation Codes4.7 Const
Page 73 and 74:
Chapter 4: Operation CodesIf a SUBS
Page 75 and 76:
Chapter 4: Operation CodesASL3 —
Page 77 and 78:
Chapter 4: Operation Codes>0 Specif
Page 79 and 80:
Chapter 4: Operation CodesThe const
Page 81 and 82:
Chapter 4: Operation Codesarg2Clear
Page 83 and 84:
Chapter 4: Operation CodesADDC —
Page 85 and 86:
Chapter 4: Operation Codesarg7Compa
Page 87 and 88:
Chapter 4: Operation CodesFor examp
Page 89 and 90:
Chapter 4: Operation Codesarg1arg2a
Page 91 and 92:
Chapter 4: Operation Codes4 Rotate
Page 93 and 94:
Chapter 4: Operation Codesarg1−1A
Page 95 and 96:
Chapter 4: Operation CodesAUOP —
Page 97 and 98:
Chapter 4: Operation CodesLMCS can
Page 99 and 100:
Chapter 4: Operation CodesLMC2 is i
Page 101 and 102:
Chapter 4: Operation Codesarg6Allow
Page 103 and 104:
Chapter 4: Operation Codes• Rings
Page 105 and 106:
Chapter 4: Operation Codesarg1Param
Page 107 and 108:
Chapter 4: Operation Codes2 H×v is
Page 109 and 110:
Chapter 4: Operation Codesarg8Spars
Page 111 and 112:
Chapter 4: Operation CodesSPMC sear
Page 113 and 114:
Chapter 4: Operation Codes0 Use set
Page 115 and 116:
Chapter 4: Operation Codes−1arg5D
Page 117 and 118:
Chapter 4: Operation Codesarg2 Line
Page 119 and 120:
Chapter 4: Operation CodesSEED —
Page 121 and 122:
Chapter 4: Operation Codesfrom with
Page 123 and 124:
Chapter 4: Operation Codesarg1-4Ato
Page 125 and 126:
Chapter 4: Operation CodesnWrite ev
Page 127 and 128:
Chapter 4: Operation Codesarg3Molec
Page 129 and 130:
Chapter 4: Operation Codes0 Time in
Page 131 and 132:
Chapter 4: Operation CodesMDAP —
Page 133 and 134:
Chapter 4: Operation CodesMHBD —
Page 135 and 136:
Chapter 4: Operation CodesMDFT —
Page 137 and 138:
Chapter 4: Operation Codesment. We
Page 139 and 140:
Chapter 4: Operation Codesarg7Time_
Page 141 and 142:
Chapter 4: Operation Codesarg6Inter
Page 143 and 144:
Chapter 4: Operation Codes1 Do not
Page 145 and 146:
Chapter 4: Operation Codesarg 8Maxi
Page 147 and 148:
Chapter 4: Operation CodesThis comm
Page 149 and 150:
Chapter 4: Operation Codes4.15 Misc
Page 151 and 152:
Chapter 4: Operation Codes45 [NEW]
Page 153 and 154:
Chapter 4: Operation Codes100 Set n
Page 155 and 156:
Chapter 4: Operation Codes252 GV, c
Page 157 and 158:
Chapter 4: Operation Codes931 Turns
Page 159 and 160:
Chapter 4: Operation Codesarg2arg3a
Page 161 and 162:
Chapter 4: Operation Codesarg1Numbe
Page 163 and 164:
Chapter 4: Operation Codes4.16 Conf
Page 165 and 166:
Chapter 4: Operation Codes−3do no
Page 167 and 168:
Chapter 4: Operation Codesarg7Minim
Page 169 and 170:
Chapter 4: Operation CodesConfGen i
Page 171 and 172:
Chapter 4: Operation Codesarg6Maxim
Page 173 and 174:
Page 175 and 176:
Chapter 5: MINTAthat energy well. N
Page 177 and 178:
Chapter 5: MINTAature. Note that H
Page 179 and 180:
Chapter 5: MINTA0 Numerical integra
Page 181 and 182:
Chapter 5: MINTAconformational sear
Page 183 and 184:
Chapter 5: MINTAtion (25,000 total
Page 185 and 186:
MacroModel Reference ManualAppendix
Page 187 and 188:
Page 189 and 190:
Page 191 and 192: Appendix C: Atom and Bond TypesTabl
Page 197 and 198: MacroModel Reference ManualAppendix
Page 199 and 200: Appendix D: Force-Field File Format
Page 231 and 232: Appendix E: The BMFF ProtocolBefore
Page 237 and 238: Appendix G: MINTA BackgroundL(s)
Page 239 and 240: Appendix G: MINTA Backgroundpath in
Page 241: Appendix G: MINTA BackgroundDirect
Page 245 and 246: MacroModel Reference ManualReferenc
Page 247 and 248: References26. Sefler, A. M.; Lauri,
Page 249 and 250: References52. Kaminski, G. A.; Frie
Page 251 and 252: Opcode IndexBold face page numbers
Page 253 and 254: Opcode IndexRRHO...................
Page 256: 120 West 45th Street, 29th FloorNew
show all

MacroModel Reference Manual - ISP

Create successful ePaper yourself

Delete template?

Save as template?