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1_polar_dipole.out
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1
Chemistry at HARvard Macromolecular Mechanics
(CHARMM) - Developmental Version 41a2 February 15, 2016
Copyright(c) 1984-2014 President and Fellows of Harvard College
All Rights Reserved
Current operating system: Linux-3.13.0-101-generic(x86_64)@strathmere.
Created on 3/26/17 at 14:06:46 by user: fylin
Maximum number of ATOMS: 360720, and RESidues: 120240
RDTITL> * ANALYSIS FOR MOLEC POLARIZABILITIES AND DIPOLE MOMENTS
RDTITL> *
CHARMM>
CHARMM> ioformat extended
MISCOM> Expanded I/O format is used.
CHARMM> ! Note: You need to change below QM dipole and alpha and put your QM results
CHARMM> ! This script will read the resi_mp2.crd
CHARMM>
CHARMM>
CHARMM> set residue clet
Parameter: RESIDUE <- "CLET"
CHARMM> ! set residue chlb
CHARMM>
CHARMM> set TOPPAR .
Parameter: TOPPAR <- "."
CHARMM> stream toppar_drude_master_example.str
VOPEN> Attempting to open::toppar_drude_master_example.str::
OPNLGU> Unit 99 opened for READONLY access to toppar_drude_master_example.str
INPUT STREAM SWITCHING TO UNIT 99
RDTITL> * $ID: TOPPAR_DRUDE_MASTER_PROTEIN.STR 22 2014-08-12 22:16:31Z ALEX $
RDTITL> * DRUDE MASTER TOPOLOGY AND PARAMETER STREAM FILE
RDTITL> * INCLUDES WATER, IONS AND 2013 PROTEIN FF RELEASE
RDTITL> * OCTOBER 2013
RDTITL> * IONS UPDATED, JUNE 2014
RDTITL> *
Parameter: IN1 <- "" <empty>
CHARMM>
CHARMM> ioformat extended
MISCOM> Expanded I/O format is used.
CHARMM>
CHARMM> !This file must be streamed prior to additional Drude FF toppar stream files
CHARMM> !and it includes parameters for the model compounds (toppar_drude_model*.str)
CHARMM>
CHARMM> !references
CHARMM> !
CHARMM> !Proteins
CHARMM> !Lopes, P.E.M., Huang, J., Shim, J., Luo, Y., Li, H., Roux, B., and
CHARMM> !MacKerell, A.D., Jr., “Polarizable Force Field for Peptides and
CHARMM> !Proteins based on the Classical Drude Oscillator,” Journal of
CHARMM> !Chemical Theory and Computation, 9: 5430–5449, 2013 DOI:
CHARMM> !10.1021/ct400781b, NIHMS53671
CHARMM> !
CHARMM> !water
CHARMM> !SWM4-NDP, negative Drude (this will be the default model): Lamoureux,
CHARMM> !G., Harder, E., Vorobyov, I.V., Deng, Y., Roux, B. MacKerell, A.D.,
CHARMM> !Jr., A polarizable model of water for molecular dynamics simulations
CHARMM> !of biomolecules, Chemical Physics Letters, 2006, 418: 245-249.
CHARMM> !
CHARMM> !SWM6: Wenbo Yu, Pedro E. M. Lopes, Benoît Roux and Alexander
CHARMM> !D. MacKerell, Jr. "Six-site Polarizable Model of Water Based on the
CHARMM> !Classical Drude Oscillator" Journal of Chemical Physics, 138: 034508,
CHARMM> !2013
CHARMM>
CHARMM> !atomic ions
CHARMM> !Yu, H., Whitfield, T.W., Harder, E., Lamoureux, G., Vorobyov, I.,
CHARMM> !Anisimov, V. M., MacKerell, A.D., Jr., and Roux, B. “Simulating
CHARMM> !Monovalent and Divalent Ions in Aqueous Solution Using a Drude
CHARMM> !Polarizable Force Field, “Journal of Chemical Theory and Computation,
CHARMM> !6: 774–786, 2010
CHARMM> !
CHARMM> !Luo, Y., Jiang, W., Yu, H., MacKerell, A.D., Jr., and Roux, B.,
CHARMM> !“Simulation study of ion pairing in concentrated aqueous salt
CHARMM> !solutions with a polarizable force field,” Faraday Discussions, 160,
CHARMM> !135–149, 2013, PMC3695446
CHARMM>
CHARMM>
CHARMM> ! note use of D for second character to indicate Drude
CHARMM> ! polarizable FF (be careful of Cadmium: use CDM)
CHARMM>
CHARMM> ! Parameter labeling after !
CHARMM> ! RESName, generic compound name of model compound followed by additional comments
CHARMM> ! for example ! BENZ, benzene, based on crystal survey data
CHARMM>
CHARMM> !Formatting information
CHARMM> !RTF section: please use the following format for future residues, including the spacing
CHARMM> !(and please clean a few up of the residues not in this format if you so desire....)
CHARMM>
CHARMM> !RESI ALA 0.000
CHARMM> !ATOM N ND2A2 -0.427 ALPHA -1.056 THOLE 0.711
CHARMM> !BOND A1 A2 A3 A4 A5 A6 A7 A8
CHARMM> !IMPR A1 A2 A3 A4
CHARMM> !CMAP A1 A2 A3 A4 A1 A2 A3 A4
CHARMM> !LONEPAIR relative A1 A2 A3 A4 distance 0.30 angle 91.00 dihe 180.00
CHARMM> !ANISOTROPY A1 A2 A3 A4 A11 0.6968 A22 1.2194
CHARMM> !IC A1 A2 A3 A4 1.3474 124.31 180.00 114.26 0.9979
CHARMM>
CHARMM> !parameter section
CHARMM> !bond
CHARMM> !CD32E OD30A 360.00 1.415 ! comment
CHARMM> !angles
CHARMM> !HDA1A CD31A CD31A 34.50 110.10 ! comment
CHARMM> !HDA1A CD31A CD31A 34.50 110.10 22.53 2.1790 ! comment
CHARMM> !dihedrals
CHARMM> !CD2O1A ND2A2 CD31C CD2O2A 0.000 3 180.00 ! comment
CHARMM> !impropers
CHARMM> !CD2O1A CD31A ND2A2 OD2C1A 120.000 0 0.00 ! comment
CHARMM> !nonbond (LJ)
CHARMM> !HDW 0.0 -0.0000 0.0000 ! comment
CHARMM> !nbfix
CHARMM> !CD30A ODW -0.00500 4.04699 ! comment
CHARMM>
CHARMM> !ioformat extended
CHARMM>
CHARMM> read rtf card !append
MAINIO> Residue topology file being read from unit 99.
RDTITL> * TOPOLOGY FOR DRUDE WATER, IONS AND PROTEINS
RDTITL> *
DRUDES PARTICLES WILL BE GENERATED AUTOMATICALLY FOR ALL ATOMS WITH NON-ZERO ALPHA
Thole-type dipole screening, Slater-Delta shape {S(u) = 1 - (1+u/2)*exp(-u)}, default radius = 1.300000
CHARMM>
CHARMM> read para card !append
PARAMETER FILE BEING READ FROM UNIT 99
RDTITL> * DRUDE POLARIZABLE FF PARAMETERS
RDTITL> *
PARRDR> WARNING: FYLIN test2 DRUD
PARRDR> WARNING: wild card for drude X
218 1 224 HDP1A DRUD 500.0000 0.0000 24977
219 2 224 HDP1B DRUD 500.0000 0.0000 24978
220 3 224 HDA1A DRUD 500.0000 0.0000 24979
221 4 224 HDA1C DRUD 500.0000 0.0000 24980
222 5 224 HDA1R5 DRUD 500.0000 0.0000 24981
223 6 224 HDA2A DRUD 500.0000 0.0000 24982
224 7 224 HDA2C DRUD 500.0000 0.0000 24983
225 8 224 HDA2E DRUD 500.0000 0.0000 24984
226 9 224 HDA2R5 DRUD 500.0000 0.0000 24985
227 10 224 HDA3A DRUD 500.0000 0.0000 24986
228 11 224 HDA3B DRUD 500.0000 0.0000 24987
229 12 224 HDA3C DRUD 500.0000 0.0000 24988
230 13 224 HDR5A DRUD 500.0000 0.0000 24989
231 14 224 HDR5B DRUD 500.0000 0.0000 24990
232 15 224 HDR5C DRUD 500.0000 0.0000 24991
233 16 224 HDR5D DRUD 500.0000 0.0000 24992
234 17 224 HDR5E DRUD 500.0000 0.0000 24993
235 18 224 HDR6A DRUD 500.0000 0.0000 24994
236 19 224 HDR6B DRUD 500.0000 0.0000 24995
237 20 224 HDR6C DRUD 500.0000 0.0000 24996
238 41 224 CD2O1A DRUD 500.0000 0.0000 25017
239 42 224 CD2O2A DRUD 500.0000 0.0000 25018
240 43 224 CD2O3A DRUD 500.0000 0.0000 25019
241 44 224 CD2O3B DRUD 500.0000 0.0000 25020
242 45 224 CD2R5A DRUD 500.0000 0.0000 25021
243 46 224 CD2R5B DRUD 500.0000 0.0000 25022
244 47 224 CD2R5C DRUD 500.0000 0.0000 25023
245 48 224 CD2R5D DRUD 500.0000 0.0000 25024
246 49 224 CD2R5E DRUD 500.0000 0.0000 25025
247 50 224 CD2R6A DRUD 500.0000 0.0000 25026
248 51 224 CD2R6B DRUD 500.0000 0.0000 25027
249 52 224 CD2R6C DRUD 500.0000 0.0000 25028
250 53 224 CD2R6D DRUD 500.0000 0.0000 25029
251 54 224 CD2R6F DRUD 500.0000 0.0000 25030
252 55 224 CD2R6H DRUD 500.0000 0.0000 25031
253 60 224 CD2N1A DRUD 500.0000 0.0000 25036
254 61 224 CD30A DRUD 500.0000 0.0000 25037
255 62 224 CD31A DRUD 500.0000 0.0000 25038
256 63 224 CD31C DRUD 500.0000 0.0000 25039
257 64 224 CD31FA DRUD 500.0000 0.0000 25040
258 65 224 CD31FB DRUD 500.0000 0.0000 25041
259 66 224 CD31FC DRUD 500.0000 0.0000 25042
260 67 224 CD31G DRUD 500.0000 0.0000 25043
261 68 224 CD315A DRUD 500.0000 0.0000 25044
262 69 224 CD315B DRUD 500.0000 0.0000 25045
263 70 224 CD316A DRUD 500.0000 0.0000 25046
264 71 224 CD32A DRUD 500.0000 0.0000 25047
265 72 224 CD32AL DRUD 500.0000 0.0000 25048
266 73 224 CD32B DRUD 500.0000 0.0000 25049
267 74 224 CD32C DRUD 500.0000 0.0000 25050
268 75 224 CD32E DRUD 500.0000 0.0000 25051
269 76 224 CD32F DRUD 500.0000 0.0000 25052
270 77 224 CD325A DRUD 500.0000 0.0000 25053
271 78 224 CD325B DRUD 500.0000 0.0000 25054
272 79 224 CD326A DRUD 500.0000 0.0000 25055
273 80 224 CD326B DRUD 500.0000 0.0000 25056
274 81 224 CD33A DRUD 500.0000 0.0000 25057
275 82 224 CD33B DRUD 500.0000 0.0000 25058
276 83 224 CD33C DRUD 500.0000 0.0000 25059
277 84 224 CD33D DRUD 500.0000 0.0000 25060
278 85 224 CD33E DRUD 500.0000 0.0000 25061
279 86 224 CD31HA DRUD 500.0000 0.0000 25062
280 87 224 CD31HB DRUD 500.0000 0.0000 25063
281 88 224 CD31HC DRUD 500.0000 0.0000 25064
282 131 224 ND2A1 DRUD 500.0000 0.0000 25107
283 132 224 ND2A2 DRUD 500.0000 0.0000 25108
284 133 224 ND2A3 DRUD 500.0000 0.0000 25109
285 134 224 ND2B1 DRUD 500.0000 0.0000 25110
286 135 224 ND2R5A DRUD 500.0000 0.0000 25111
287 136 224 ND2R5B DRUD 500.0000 0.0000 25112
288 137 224 ND2R5C DRUD 500.0000 0.0000 25113
289 138 224 ND2R5D DRUD 500.0000 0.0000 25114
290 139 224 ND2R5E DRUD 500.0000 0.0000 25115
291 140 224 ND2R5F DRUD 500.0000 0.0000 25116
292 141 224 ND2R6A DRUD 500.0000 0.0000 25117
293 142 224 ND2R6B DRUD 500.0000 0.0000 25118
294 143 224 ND2R6C DRUD 500.0000 0.0000 25119
295 144 224 ND2R6D DRUD 500.0000 0.0000 25120
296 145 224 ND2P1A DRUD 500.0000 0.0000 25121
297 146 224 ND3P2A DRUD 500.0000 0.0000 25122
298 147 224 ND3P3A DRUD 500.0000 0.0000 25123
299 148 224 ND3A3 DRUD 500.0000 0.0000 25124
300 171 224 OD2C1A DRUD 500.0000 0.0000 25147
301 172 224 OD2C1B DRUD 500.0000 0.0000 25148
302 173 224 OD2C2A DRUD 500.0000 0.0000 25149
303 174 224 OD2C2B DRUD 500.0000 0.0000 25150
304 175 224 OD2C2C DRUD 500.0000 0.0000 25151
305 176 224 OD2C3A DRUD 500.0000 0.0000 25152
306 177 224 OD2C3B DRUD 500.0000 0.0000 25153
307 178 224 OD30A DRUD 500.0000 0.0000 25154
308 179 224 OD30B DRUD 500.0000 0.0000 25155
309 180 224 OD30BN DRUD 500.0000 0.0000 25156
310 181 224 OD30C DRUD 500.0000 0.0000 25157
311 182 224 OD30CL DRUD 500.0000 0.0000 25158
312 183 224 OD30D DRUD 500.0000 0.0000 25159
313 184 224 OD305A DRUD 500.0000 0.0000 25160
314 185 224 OD306A DRUD 500.0000 0.0000 25161
315 186 224 OD31A DRUD 500.0000 0.0000 25162
316 187 224 OD31B DRUD 500.0000 0.0000 25163
317 188 224 OD31C DRUD 500.0000 0.0000 25164
318 189 224 OD31E DRUD 500.0000 0.0000 25165
319 190 224 OD31F DRUD 500.0000 0.0000 25166
320 211 224 PD1A DRUD 500.0000 0.0000 25187
321 212 224 PD1AN DRUD 500.0000 0.0000 25188
322 221 224 DUM DRUD 500.0000 0.0000 25197
323 222 224 XED DRUD 500.0000 0.0000 25198
324 223 224 NED DRUD 500.0000 0.0000 25199
325 224 224 DRUD DRUD 500.0000 0.0000 25200
326 226 224 SD31A DRUD 500.0000 0.0000 25649
327 227 224 SD31B DRUD 500.0000 0.0000 25875
328 228 224 SD30A DRUD 500.0000 0.0000 26102
329 229 224 SD30B DRUD 500.0000 0.0000 26330
330 231 224 LPD DRUD 500.0000 0.0000 26789
331 232 224 LPDW DRUD 500.0000 0.0000 27020
332 233 224 LPDO1 DRUD 500.0000 0.0000 27252
333 234 224 LPDNA1 DRUD 500.0000 0.0000 27485
334 241 224 ODW DRUD 500.0000 0.0000 29144
335 242 224 ODW6 DRUD 500.0000 0.0000 29385
336 243 224 HDW DRUD 500.0000 0.0000 29627
337 244 224 DOH2 DRUD 500.0000 0.0000 29870
338 251 224 LID DRUD 500.0000 0.0000 31599
339 252 224 POTD DRUD 500.0000 0.0000 31850
340 253 224 SODD DRUD 500.0000 0.0000 32102
341 254 224 RBD DRUD 500.0000 0.0000 32355
342 255 224 CSD DRUD 500.0000 0.0000 32609
343 256 224 FAD DRUD 500.0000 0.0000 32864
344 257 224 CLAD DRUD 500.0000 0.0000 33120
345 258 224 BRAD DRUD 500.0000 0.0000 33377
346 259 224 IAD DRUD 500.0000 0.0000 33635
347 271 224 MAGD DRUD 500.0000 0.0000 36809
348 272 224 CALD DRUD 500.0000 0.0000 37080
349 273 224 SRD DRUD 500.0000 0.0000 37352
350 274 224 BAD DRUD 500.0000 0.0000 37625
351 275 224 ZND DRUD 500.0000 0.0000 37899
352 282 224 CLDA1 DRUD 500.0000 0.0000 39845
353 283 224 CLDR1 DRUD 500.0000 0.0000 40127
PARRDR> WARNING: ATOMS IN BOND X DRUD 500.00000 0.00000 DONT EXIST
THOLE CUTOFF 5.000
MAXNBTHOLE -5000
Pair-specific Thole: 1 ODW BAD 1.4586900000000000 241 274
Pair-specific Thole: 2 ODW CALD 1.5087699999999999 241 272
Pair-specific Thole: 3 ODW MAGD 1.5156700000000001 241 271
Pair-specific Thole: 4 ODW SRD 1.2379199999999999 241 273
Pair-specific Thole: 5 ODW ZND 2.1477300000000001 241 275
Pair-specific Thole: 6 CALD OD2C1A 1.3200000000000001 272 171
Pair-specific Thole: 7 CALD OD31A 1.0500000000000000 272 186
Pair-specific Thole: 8 SODD OD31A 1.8200000000000001 253 186
Pair-specific Thole: 9 POTD OD2C1A 2.1899999999999999 252 171
Pair-specific Thole: 10 POTD OD2C2A 0.22000000000000000 252 173
Pair-specific Thole: 11 CLAD ND2A2 2.8599999999999999 257 132
***** WARNING ***** PARRDR no nonbond parameters for atom type: 282 CLDA1
NO nonbond interactions will be computed for this atom type.
***** WARNING ***** PARRDR no nonbond parameters for atom type: 283 CLDR1
NO nonbond interactions will be computed for this atom type.
PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared.
CHARMM>
VCLOSE: Closing unit 99 with status "KEEP"
RETURNING TO INPUT STREAM 5
CHARMM> stream toppar_drude_example.str
VOPEN> Attempting to open::toppar_drude_example.str::
OPNLGU> Unit 99 opened for READONLY access to toppar_drude_example.str
INPUT STREAM SWITCHING TO UNIT 99
RDTITL> * TOPPAR STREAM FILE FOR TUTORIAL
RDTITL> *
Parameter: IN1 <- "" <empty>
CHARMM>
CHARMM> ioformat extended
MISCOM> Expanded I/O format is used.
CHARMM>
CHARMM> read rtf card append
MAINIO> Residue topology file being read from unit 99.
RDTITL> * TOPOLOGY FOR DRUDE MODEL COMPOUNDS
RDTITL> *
DRUDES PARTICLES WILL BE GENERATED AUTOMATICALLY FOR ALL ATOMS WITH NON-ZERO ALPHA
Thole-type dipole screening, Slater-Delta shape {S(u) = 1 - (1+u/2)*exp(-u)}, default radius = 1.300000
CHARMM>
CHARMM> read para card append
PARAMETER FILE BEING READ FROM UNIT 99
RDTITL> * HALOGEN
RDTITL> *
PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared.
CHARMM> RETURN
VCLOSE: Closing unit 99 with status "KEEP"
RETURNING TO INPUT STREAM 5
CHARMM>
CHARMM> ! qm optimized @resi_mp.crd
CHARMM> set mp2dir ./gauss_opt
Parameter: MP2DIR <- "./GAUSS_OPT"
CHARMM>
CHARMM> !non-bond parameters
CHARMM> set 3 999.0 ! cutim
Parameter: 3 <- "999.0"
CHARMM> set 4 999.0 ! cutnb
Parameter: 4 <- "999.0"
CHARMM> set 5 980.0 ! ctonnb
Parameter: 5 <- "980.0"
CHARMM> set 6 990.0 ! ctofnb
Parameter: 6 <- "990.0"
CHARMM> set 7 switch
Parameter: 7 <- "SWITCH"
CHARMM> set 8 atom
Parameter: 8 <- "ATOM"
CHARMM> set 9 vatom
Parameter: 9 <- "VATOM"
CHARMM>
CHARMM> read sequence @residue 1
Parameter: RESIDUE -> "CLET"
CHARMM> generate @residue first none last none setup warn drude dmass 0.4
Parameter: RESIDUE -> "CLET"
Drude polarizability will be setup for SEGID: CLET mass of Drudes particles = 0.4000
NO PATCHING WILL BE DONE ON THE FIRST RESIDUE
NO PATCHING WILL BE DONE ON THE LAST RESIDUE
MKDRUDE generate list and setup for drude polarizability
All okay for 3 added Drude particles
GENPSF> Segment 1 has been generated. Its identifier is CLET.
PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
PSFSUM> Summary of the structure file counters :
Number of segments = 1 Number of residues = 1
Number of atoms = 12 Number of groups = 1
Number of bonds = 11 Number of angles = 12
Number of dihedrals = 9 Number of impropers = 0
Number of cross-terms = 0
Number of HB acceptors = 0 Number of HB donors = 0
Number of NB exclusions = 0 Total charge = 0.00000
Number of Drudes = 3
Number of true-bonds = 11 Number of zero-bonds = 0
Number of aniso. terms = 0 Number of lone-pairs = 1
CHARMM> bomlev 0
CHARMM>
CHARMM> open read card unit 21 name @mp2dir/@residue_mp2.crd
Parameter: MP2DIR -> "./GAUSS_OPT"
Parameter: RESIDUE -> "CLET"
VOPEN> Attempting to open::./gauss_opt/clet_mp2.crd::
OPNLGU> Unit 21 opened for READONLY access to ./gauss_opt/clet_mp2.crd
CHARMM> read coor card unit 21
SPATIAL COORDINATES BEING READ FROM UNIT 21
TITLE> 8 EXT
RDTITL> No title read.
** WARNING ** After reading, there are no coordinates for selected atom: 2 1 CLET DC1
** WARNING ** After reading, there are no coordinates for selected atom: 4 1 CLET DCL11
** WARNING ** After reading, there are no coordinates for selected atom: 5 1 CLET LP
** WARNING ** After reading, there are no coordinates for selected atom: 9 1 CLET DC2
** A total of 4 selected atoms have no coordinates
*** LEVEL 2 WARNING *** BOMLEV IS 0
CHARMM>
CHARMM> coor sdrude
CHARMM> coor shake
SELECTED COORDINATES CONSTRAINED IN THE MAIN SET.
CHARMM> coor copy comp
SELECTED COORDINATES COPIED TO THE COMPARISON SET.
CHARMM>
CHARMM> update cdie inbfrq -1 ihbfrq 0 -
CHARMM> @7 @8 @9 vswitch cutnb @4 ctofnb @6 ctonnb @5
Parameter: 7 -> "SWITCH"
Parameter: 8 -> "ATOM"
Parameter: 9 -> "VATOM"
Parameter: 4 -> "999.0"
Parameter: 6 -> "990.0"
Parameter: 5 -> "980.0"
NONBOND OPTION FLAGS:
ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch
BYGRoup NOEXtnd NOEWald
CUTNB =999.000 CTEXNB =999.000 CTONNB =980.000 CTOFNB =990.000
CGONNB = 0.000 CGOFNB = 10.000
WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000
NBXMOD = 5
There are 0 atom pairs and 0 atom exclusions.
There are 0 group pairs and 0 group exclusions.
<MAKINB> with mode 5 found 51 exclusions and 15 interactions(1-4)
<MAKGRP> found 0 group exclusions.
Generating nonbond list with Exclusion mode = 5
Allocate space for 5000 Thole shielding pairs
== PRIMARY == SPACE FOR 289 ATOM PAIRS AND 0 GROUP PAIRS
General atom nonbond list generation found:
15 ATOM PAIRS WERE FOUND FOR ATOM LIST
0 GROUP PAIRS REQUIRED ATOM SEARCHES
CHARMM>
CHARMM> cons harm force 10000000.0 sele .not. type D* show end
The following atoms are currently set:
SEGId RESId RESName .. TYPEs ..
CLET 1 CLET C1 CL11 LP H12 H13 C2 H21 H22 H23
SELRPN> 9 atoms have been selected out of 12
CSTRAN: Harmonic Restraints
ABSOlute type as set number 1. Number of selected atoms: 9
Reference coordinates set to main coordinates.
Mass weighting will NOT be used for new restraints.
The force constant of10000000.00000 will be used.
An exponent of 2 will be used.
The XYZ scale factors are: 1.00000 1.00000 1.00000
A total of 9 atoms are restrained.
CHARMM> cons harm force 10000000.0 sele type dum show end
The following atoms are currently set:
SEGId RESId RESName .. TYPEs ..
SELRPN> 0 atoms have been selected out of 12
CSTRAN: Harmonic Restraints
ABSOlute type as set number 2. Number of selected atoms: 0
Reference coordinates set to main coordinates.
Mass weighting will NOT be used for new restraints.
The force constant of10000000.00000 will be used.
An exponent of 2 will be used.
The XYZ scale factors are: 1.00000 1.00000 1.00000
A total of 9 atoms are restrained.
CHARMM> MINI SD nstep 200 tolgrd 0.00001
NONBOND OPTION FLAGS:
ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch
BYGRoup NOEXtnd NOEWald
CUTNB =999.000 CTEXNB =999.000 CTONNB =980.000 CTOFNB =990.000
CGONNB = 0.000 CGOFNB = 10.000
WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000
NBXMOD = 5
There are 15 atom pairs and 66 atom exclusions.
There are 0 group pairs and 0 group exclusions.
Generating nonbond list with Exclusion mode = 5
== PRIMARY == SPACE FOR 289 ATOM PAIRS AND 0 GROUP PAIRS
General atom nonbond list generation found:
15 ATOM PAIRS WERE FOUND FOR ATOM LIST
0 GROUP PAIRS REQUIRED ATOM SEARCHES
STEEPD> An energy minimization has been requested.
NSTEP = 200 NPRINT = 10
STEP = 0.0200000 TOLFUN = 0.0000000
TOLGRD = 0.0000100 TOLSTP = 0.0000000
MINI MIN: Cycle ENERgy Delta-E GRMS Step-size
MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers
MINI EXTERN: VDWaals ELEC HBONds ASP USER
---------- --------- --------- --------- --------- ---------
MINI> 0 -2.17290 0.00000 5.08051 0.02000
MINI INTERN> 0.27227 0.24533 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.50851 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 10 1505.27488 -1507.44778 99816.19035 0.00156
MINI INTERN> 0.74619 0.25414 0.02639 0.00333 0.00000
MINI EXTERN> -0.21199 -2.95384 0.00000 0.00000 0.00000
MINI CONSTR> 1507.41065 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 20 -1.12139 1506.39627 2648.18828 0.00012
MINI INTERN> 0.65702 0.24515 0.02268 0.00354 0.00000
MINI EXTERN> -0.20819 -2.90342 0.00000 0.00000 0.00000
MINI CONSTR> 1.06184 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 30 -1.33899 0.21760 2361.21880 0.00002
MINI INTERN> 0.65704 0.24517 0.02269 0.00354 0.00000
MINI EXTERN> -0.20820 -2.90350 0.00000 0.00000 0.00000
MINI CONSTR> 0.84427 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 40 -2.17703 0.83804 191.24578 0.00000
MINI INTERN> 0.65851 0.24531 0.02276 0.00354 0.00000
MINI EXTERN> -0.20828 -2.90448 0.00000 0.00000 0.00000
MINI CONSTR> 0.00562 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 50 -2.18217 0.00513 54.30393 0.00000
MINI INTERN> 0.65853 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.90451 0.00000 0.00000 0.00000
MINI CONSTR> 0.00049 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 60 -2.18266 0.00049 9.47453 0.00000
MINI INTERN> 0.65846 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.90450 0.00000 0.00000 0.00000
MINI CONSTR> 0.00004 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 70 -2.18271 0.00005 9.12926 0.00000
MINI INTERN> 0.65837 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.90446 0.00000 0.00000 0.00000
MINI CONSTR> 0.00004 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 80 -2.18276 0.00005 10.01854 0.00000
MINI INTERN> 0.65829 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.90443 0.00000 0.00000 0.00000
MINI CONSTR> 0.00004 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 90 -2.18281 0.00005 10.73063 0.00000
MINI INTERN> 0.65820 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.90439 0.00000 0.00000 0.00000
MINI CONSTR> 0.00004 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 100 -2.18288 0.00007 3.75282 0.00000
MINI INTERN> 0.65812 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.90436 0.00000 0.00000 0.00000
MINI CONSTR> 0.00002 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 110 -2.18293 0.00005 2.69357 0.00000
MINI INTERN> 0.65803 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.90433 0.00000 0.00000 0.00000
MINI CONSTR> 0.00002 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 120 -2.18299 0.00006 2.77784 0.00000
MINI INTERN> 0.65794 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.90429 0.00000 0.00000 0.00000
MINI CONSTR> 0.00002 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 130 -2.18304 0.00005 3.47850 0.00000
MINI INTERN> 0.65785 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.90425 0.00000 0.00000 0.00000
MINI CONSTR> 0.00002 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 140 -2.18309 0.00006 3.64892 0.00000
MINI INTERN> 0.65776 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.90422 0.00000 0.00000 0.00000
MINI CONSTR> 0.00002 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 150 -2.18314 0.00005 6.87076 0.00000
MINI INTERN> 0.65767 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.90418 0.00000 0.00000 0.00000
MINI CONSTR> 0.00003 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 160 -2.18320 0.00005 7.28082 0.00000
MINI INTERN> 0.65758 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.90415 0.00000 0.00000 0.00000
MINI CONSTR> 0.00003 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 170 -2.18325 0.00005 8.70475 0.00000
MINI INTERN> 0.65749 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.90411 0.00000 0.00000 0.00000
MINI CONSTR> 0.00003 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 180 -2.18330 0.00005 8.64547 0.00000
MINI INTERN> 0.65741 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.90408 0.00000 0.00000 0.00000
MINI CONSTR> 0.00003 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 190 -2.18335 0.00005 9.08066 0.00000
MINI INTERN> 0.65731 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.90404 0.00000 0.00000 0.00000
MINI CONSTR> 0.00003 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 200 -2.18340 0.00005 9.94643 0.00000
MINI INTERN> 0.65723 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.90401 0.00000 0.00000 0.00000
MINI CONSTR> 0.00003 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
STEEPD> Minimization exiting with number of steps limit ( 200) exceeded.
STPD MIN: Cycle ENERgy Delta-E GRMS Step-size
STPD INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers
STPD EXTERN: VDWaals ELEC HBONds ASP USER
STPD CONSTR: HARMonic CDIHedral CIC RESDistance NOE
---------- --------- --------- --------- --------- ---------
STPD> 200 -2.18340 0.00005 9.94643 0.00000
STPD INTERN> 0.65723 0.24532 0.02277 0.00354 0.00000
STPD EXTERN> -0.20829 -2.90401 0.00000 0.00000 0.00000
STPD CONSTR> 0.00003 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
CHARMM> MINI ABNR nstep 500 tolgrd 0.00001
NONBOND OPTION FLAGS:
ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch
BYGRoup NOEXtnd NOEWald
CUTNB =999.000 CTEXNB =999.000 CTONNB =980.000 CTOFNB =990.000
CGONNB = 0.000 CGOFNB = 10.000
WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000
NBXMOD = 5
There are 15 atom pairs and 66 atom exclusions.
There are 0 group pairs and 0 group exclusions.
Generating nonbond list with Exclusion mode = 5
== PRIMARY == SPACE FOR 289 ATOM PAIRS AND 0 GROUP PAIRS
General atom nonbond list generation found:
15 ATOM PAIRS WERE FOUND FOR ATOM LIST
0 GROUP PAIRS REQUIRED ATOM SEARCHES
ABNER> An energy minimization has been requested.
EIGRNG = 0.0005000 MINDIM = 5
NPRINT = 10 NSTEP = 500
PSTRCT = 0.0000000 SDSTP = 0.0200000
STPLIM = 1.0000000 STRICT = 0.1000000
TOLFUN = 0.0000000 TOLGRD = 0.0000100
TOLITR = 100 TOLSTP = 0.0000000
FMEM = 0.0000000
MINI MIN: Cycle ENERgy Delta-E GRMS Step-size
MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers
MINI EXTERN: VDWaals ELEC HBONds ASP USER
MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE
---------- --------- --------- --------- --------- ---------
MINI> 0 -2.18340 0.00000 8.21692 0.00000
MINI INTERN> 0.65723 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.90400 0.00000 0.00000 0.00000
MINI CONSTR> 0.00004 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 10 6.03489 -8.21829 7371.00615 0.00041
MINI INTERN> 0.65934 0.24583 0.02302 0.00352 0.00000
MINI EXTERN> -0.20857 -2.90618 0.00000 0.00000 0.00000
MINI CONSTR> 8.21792 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 20 -0.70072 6.73560 2112.85799 0.00030
MINI INTERN> 0.63533 0.24534 0.02265 0.00352 0.00000
MINI EXTERN> -0.20806 -2.89592 0.00000 0.00000 0.00000
MINI CONSTR> 1.49641 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 30 -2.18129 1.48057 274.92139 0.00004
MINI INTERN> 0.64058 0.24530 0.02277 0.00354 0.00000
MINI EXTERN> -0.20828 -2.89705 0.00000 0.00000 0.00000
MINI CONSTR> 0.01186 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 40 -2.16831 -0.01298 403.37601 0.00003
MINI INTERN> 0.63962 0.24535 0.02277 0.00353 0.00000
MINI EXTERN> -0.20830 -2.89686 0.00000 0.00000 0.00000
MINI CONSTR> 0.02558 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 50 -2.19380 0.02549 37.53384 0.00001
MINI INTERN> 0.63861 0.24533 0.02277 0.00353 0.00000
MINI EXTERN> -0.20829 -2.89639 0.00000 0.00000 0.00000
MINI CONSTR> 0.00063 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 60 -2.19524 0.00144 23.97521 0.00000
MINI INTERN> 0.63673 0.24532 0.02276 0.00354 0.00000
MINI EXTERN> -0.20829 -2.89552 0.00000 0.00000 0.00000
MINI CONSTR> 0.00022 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 70 -2.27510 0.07986 70.28771 0.00001
MINI INTERN> 0.42120 0.24533 0.02277 0.00354 0.00000
MINI EXTERN> -0.20828 -2.76100 0.00000 0.00000 0.00000
MINI CONSTR> 0.00135 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 80 -2.27633 0.00122 10.95687 0.00000
MINI INTERN> 0.42298 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.76269 0.00000 0.00000 0.00000
MINI CONSTR> 0.00005 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 90 -2.27639 0.00006 5.12632 0.00000
MINI INTERN> 0.42295 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.76269 0.00000 0.00000 0.00000
MINI CONSTR> 0.00002 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 100 -2.27741 0.00103 21.17864 0.00000
MINI INTERN> 0.41472 0.24533 0.02277 0.00353 0.00000
MINI EXTERN> -0.20829 -2.75585 0.00000 0.00000 0.00000
MINI CONSTR> 0.00037 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 110 -2.27896 0.00155 25.57855 0.00000
MINI INTERN> 0.39675 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.73916 0.00000 0.00000 0.00000
MINI CONSTR> 0.00012 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 120 -2.27906 0.00010 3.58140 0.00000
MINI INTERN> 0.39680 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.73922 0.00000 0.00000 0.00000
MINI CONSTR> 0.00002 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 130 -2.27906 0.00000 0.67288 0.00000
MINI INTERN> 0.39679 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.73921 0.00000 0.00000 0.00000
MINI CONSTR> 0.00002 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 140 -2.27913 0.00006 5.11966 0.00000
MINI INTERN> 0.39422 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.73671 0.00000 0.00000 0.00000
MINI CONSTR> 0.00003 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 150 -2.27916 0.00003 2.02537 0.00000
MINI INTERN> 0.39187 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.73437 0.00000 0.00000 0.00000
MINI CONSTR> 0.00001 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 160 -2.27916 0.00000 1.71550 0.00000
MINI INTERN> 0.39190 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.73441 0.00000 0.00000 0.00000
MINI CONSTR> 0.00002 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 170 -2.27916 0.00000 0.52021 0.00000
MINI INTERN> 0.39207 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.73458 0.00000 0.00000 0.00000
MINI CONSTR> 0.00001 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 180 -2.27916 0.00000 0.03905 0.00000
MINI INTERN> 0.39212 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.73463 0.00000 0.00000 0.00000
MINI CONSTR> 0.00001 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 190 -2.27916 0.00000 0.92756 0.00000
MINI INTERN> 0.39145 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.73397 0.00000 0.00000 0.00000
MINI CONSTR> 0.00001 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 200 -2.27916 0.00000 0.15222 0.00000
MINI INTERN> 0.39145 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.73397 0.00000 0.00000 0.00000
MINI CONSTR> 0.00001 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 210 -2.27916 0.00000 0.05282 0.00000
MINI INTERN> 0.39139 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.73390 0.00000 0.00000 0.00000
MINI CONSTR> 0.00001 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 220 -2.27916 0.00000 0.36539 0.00000
MINI INTERN> 0.39103 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.73354 0.00000 0.00000 0.00000
MINI CONSTR> 0.00001 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 230 -2.27916 0.00000 0.32986 0.00000
MINI INTERN> 0.39093 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.73344 0.00000 0.00000 0.00000
MINI CONSTR> 0.00001 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 240 -2.27916 0.00000 0.02189 0.00000
MINI INTERN> 0.39092 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.73344 0.00000 0.00000 0.00000
MINI CONSTR> 0.00001 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 250 -2.27916 0.00000 0.00673 0.00000
MINI INTERN> 0.39092 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.73344 0.00000 0.00000 0.00000
MINI CONSTR> 0.00001 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 260 -2.27916 0.00000 0.00867 0.00000
MINI INTERN> 0.39092 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.73344 0.00000 0.00000 0.00000
MINI CONSTR> 0.00001 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 270 -2.27916 0.00000 0.00301 0.00000
MINI INTERN> 0.39092 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.73344 0.00000 0.00000 0.00000
MINI CONSTR> 0.00001 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 280 -2.27916 0.00000 0.00073 0.00000
MINI INTERN> 0.39092 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.73344 0.00000 0.00000 0.00000
MINI CONSTR> 0.00001 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 290 -2.27916 0.00000 0.00026 0.00000
MINI INTERN> 0.39092 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.73344 0.00000 0.00000 0.00000
MINI CONSTR> 0.00001 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 300 -2.27916 -0.00000 0.00018 0.00000
MINI INTERN> 0.39092 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.73344 0.00000 0.00000 0.00000
MINI CONSTR> 0.00001 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 310 -2.27916 0.00000 0.00017 0.00000
MINI INTERN> 0.39092 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.73344 0.00000 0.00000 0.00000
MINI CONSTR> 0.00001 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 320 -2.27916 -0.00000 0.00016 0.00000
MINI INTERN> 0.39092 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.73344 0.00000 0.00000 0.00000
MINI CONSTR> 0.00001 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 330 -2.27916 0.00000 0.00016 0.00000
MINI INTERN> 0.39092 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.73344 0.00000 0.00000 0.00000
MINI CONSTR> 0.00001 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 340 -2.27916 -0.00000 0.00015 0.00000
MINI INTERN> 0.39092 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.73344 0.00000 0.00000 0.00000
MINI CONSTR> 0.00001 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 350 -2.27916 0.00000 0.00015 0.00000
MINI INTERN> 0.39092 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.73344 0.00000 0.00000 0.00000
MINI CONSTR> 0.00001 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 360 -2.27916 0.00000 0.00015 0.00000
MINI INTERN> 0.39092 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.73344 0.00000 0.00000 0.00000
MINI CONSTR> 0.00001 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 370 -2.27916 0.00000 0.00014 0.00000
MINI INTERN> 0.39092 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.73344 0.00000 0.00000 0.00000
MINI CONSTR> 0.00001 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 380 -2.27916 -0.00000 0.00014 0.00000
MINI INTERN> 0.39092 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.73344 0.00000 0.00000 0.00000
MINI CONSTR> 0.00001 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 390 -2.27916 -0.00000 0.00023 0.00000
MINI INTERN> 0.39092 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.73344 0.00000 0.00000 0.00000
MINI CONSTR> 0.00001 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 400 -2.27916 0.00000 0.00022 0.00000
MINI INTERN> 0.39092 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.73344 0.00000 0.00000 0.00000
MINI CONSTR> 0.00001 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 410 -2.27916 -0.00000 0.00021 0.00000
MINI INTERN> 0.39092 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.73344 0.00000 0.00000 0.00000
MINI CONSTR> 0.00001 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 420 -2.27916 0.00000 0.00019 0.00000
MINI INTERN> 0.39092 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.73344 0.00000 0.00000 0.00000
MINI CONSTR> 0.00001 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 430 -2.27916 0.00000 0.00019 0.00000
MINI INTERN> 0.39092 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.73344 0.00000 0.00000 0.00000
MINI CONSTR> 0.00001 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 440 -2.27916 -0.00000 0.00018 0.00000
MINI INTERN> 0.39092 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.73344 0.00000 0.00000 0.00000
MINI CONSTR> 0.00001 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 450 -2.27916 0.00000 0.00018 0.00000
MINI INTERN> 0.39092 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.73344 0.00000 0.00000 0.00000
MINI CONSTR> 0.00001 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 460 -2.27916 -0.00000 0.00018 0.00000
MINI INTERN> 0.39092 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.73344 0.00000 0.00000 0.00000
MINI CONSTR> 0.00001 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 470 -2.27916 0.00000 0.00017 0.00000
MINI INTERN> 0.39092 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.73344 0.00000 0.00000 0.00000
MINI CONSTR> 0.00001 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 480 -2.27916 0.00000 0.00016 0.00000
MINI INTERN> 0.39092 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.73344 0.00000 0.00000 0.00000
MINI CONSTR> 0.00001 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 490 -2.27916 -0.00000 0.00016 0.00000
MINI INTERN> 0.39092 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.73344 0.00000 0.00000 0.00000
MINI CONSTR> 0.00001 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
MINI> 500 -2.27916 0.00000 0.00015 0.00000
MINI INTERN> 0.39092 0.24532 0.02277 0.00354 0.00000
MINI EXTERN> -0.20829 -2.73344 0.00000 0.00000 0.00000
MINI CONSTR> 0.00001 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
ABNER> Minimization exiting with number of steps limit ( 500) exceeded.
ABNR MIN: Cycle ENERgy Delta-E GRMS Step-size
ABNR INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers
ABNR EXTERN: VDWaals ELEC HBONds ASP USER
ABNR CONSTR: HARMonic CDIHedral CIC RESDistance NOE
---------- --------- --------- --------- --------- ---------
ABNR> 500 -2.27916 0.00000 0.00015 0.00000
ABNR INTERN> 0.39092 0.24532 0.02277 0.00354 0.00000
ABNR EXTERN> -0.20829 -2.73344 0.00000 0.00000 0.00000
ABNR CONSTR> 0.00001 0.00000 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
CHARMM> cons harm force 0.0 sele all end
SELRPN> 12 atoms have been selected out of 12
CSTRAN: Harmonic Restraints
ABSOlute type as set number 1. Number of selected atoms: 12
Reference coordinates set to main coordinates.
Mass weighting will NOT be used for new restraints.
The force constant of 0.00000 will be used.
An exponent of 2 will be used.
The XYZ scale factors are: 1.00000 1.00000 1.00000
A total of 0 atoms are restrained.
CHARMM>
CHARMM> MINI SD nstep 200 tolgrd 0.00001
NONBOND OPTION FLAGS:
ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch
BYGRoup NOEXtnd NOEWald
CUTNB =999.000 CTEXNB =999.000 CTONNB =980.000 CTOFNB =990.000
CGONNB = 0.000 CGOFNB = 10.000
WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000
NBXMOD = 5
There are 15 atom pairs and 66 atom exclusions.
There are 0 group pairs and 0 group exclusions.
Generating nonbond list with Exclusion mode = 5
== PRIMARY == SPACE FOR 289 ATOM PAIRS AND 0 GROUP PAIRS
General atom nonbond list generation found:
15 ATOM PAIRS WERE FOUND FOR ATOM LIST
0 GROUP PAIRS REQUIRED ATOM SEARCHES
STEEPD> An energy minimization has been requested.
NSTEP = 200 NPRINT = 10
STEP = 0.0200000 TOLFUN = 0.0000000
TOLGRD = 0.0000100 TOLSTP = 0.0000000
MINI MIN: Cycle ENERgy Delta-E GRMS Step-size
MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers