MacroModel Reference Manual - ISP

More documents

Recommendations

Info

Chapter 4: Operation Codesarg2Outer atom0 All bends with arg1 as the central atom with be replaced with vdW interactions.>0 Arg3 must also be greater than 0. In this situation, the arg2-arg1-arg3 bond will bereplaced by a vdW interaction.
Chapter 4: Operation CodesIf solvation is used in a minimization, the structure is minimized with analytical approximationsto surface areas, but the final energies reported use accurate numerical areas.If energies change substantially on reminimization or nonbonded updates, use the EXNBcommand to increase the nonbonded cutoff distances for electrostatics and van der Waals.Alternatively, update more frequently using arg7.arg1Minimization mode0.5 kJ/Å-mol.9 Truncated Newton (TNCG)—Superb method for flexible structures. There is nolimit on the number of atoms in the molecule when using TNCG. [24]. See arg6.10 Limited Broyden-Fletcher-Goldfarb-Shanno (LBFGS)—LBFGS can be specifiedby MINI arg1=10. Experiments so far have not shown superiority of this methodabove all others; however, we expect to improve the implementation as time goeson, as we feel this method has great potential.11 LTNCG—LTNCG is virtually identical to TNCG (MINI arg1=9), but it requires lessmemory and thus can be used on larger molecules. Differences between TNCG andLTNCG:TNCG is effectively single precision, but LTNCG is fully double precision.Because of the difference between the Hessian cutoff used by TNCG and LTNCG(see ARPK arg8), and the limited memory allowed for Hessian storage in LTNCG(see ARPK arg4), the sparse Hessian representation of TNCG and LTNCG mightdiffer. Nevertheless, LTNCG gives practically identical results with TNCG on smallto medium sized molecules (up to approx. 1000 atoms).For molecules for which both TNCG and LTNCG can be used, TNCG is faster by afactor of approx. 1.5 to 2.MacroModel 9.7 Reference Manual 53
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 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 37 and 38: Chapter 3: Running MacroModel with
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: Chapter 4: Operation Codes
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:
MacroModel Reference ManualChapter
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 193 and 194:
Page 195 and 196:
Page 197 and 198:
Page 199 and 200:
Appendix D: Force-Field File Format
Page 201 and 202:
Page 203 and 204:
Page 205 and 206:
Page 207 and 208:
Page 209 and 210:
Page 211 and 212:
Page 213 and 214:
Page 215 and 216:
Page 217 and 218:
Page 219 and 220:
Page 221 and 222:
Page 223 and 224:
Page 225 and 226:
Page 227 and 228:
Page 229 and 230:
Page 231 and 232:
Appendix E: The BMFF ProtocolBefore
Page 233 and 234:
Page 235 and 236:
Page 237 and 238:
Appendix G: MINTA BackgroundL(s)
Page 239 and 240:
Appendix G: MINTA Backgroundpath in
Page 241 and 242:
Appendix G: MINTA BackgroundDirect
Page 243 and 244:
Appendix G: MINTA BackgroundPaulsen
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?