source: README

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Initial import to BerliOS corresponding to 3.0.4

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1README
2
3The SMMP package is designed for molecular simulation of linear
4proteins within the standard geometry model. The package contains
5various modern Monte Carlo algorithms and energy minimization
6routines. The energy of the protein can be calculated by exploiting
7one of three force fields: ECEPP/2, ECEPP/3 or FLEX. Two subroutines
8are included for approximating protein-solvent interaction by means
9of calculating the solvent accessible area of atomic groups (either
10analytically or in an approximate way). More information on SMMP can
11be found in the manual (file `manual.ps'), our papers (F. Eisenmenger,
12U.H.E. Hansmann, S. Hayryan and C.K. Hu, [SMMP] A Modern Package for
13Protein Simulations, Comp.Phys. Comm. (2001), 138 (2001) 192-212;
14[SMMP 1.1] - An Enhanced Open-Source Software Package, submitted), and
15on the SMMP homepage: http://www.smmp05.net
16
17SMMP is offered as open code. We encourage users to re-write code,
18or add their own modules, whenever they see the need. For terms of
19use of SMMP, please see the manual (manual.pdf) and the license
20agreement (license.txt). By viewing or using any part of SMMP you
21agree with the terms of the license. Any suggestions for improvement
22of the code or reports on bugs are welcome.
23
24Please send your remarks to:
25- Frank Eisenmenger: eisenmenger@fmp-berlin.de
26- Ulrich H.E. Hansmann: hansmann@mtu.edu
27- Shura Hayryan: shura@phys.sinica.edu.tw
28- Chin-Kun Hu: huck@phys.sinica.edu.tw
29- Jan H. Meinke j.meinke@fz-juelich.de
30
31
32
332) INSTALLATION:
34After uncompressing and un-tar-ing the SMMP package into a separate
35directory, the following files should be in that directory:
36
37- README This README-file
38
39- SMMP A sub-directory containing:
40 - lib.sh2 Library file with ECEPP/2 parameters
41 - lib.sh3 Library file with ECEPP/3 parameters
42 - lib.flex Library file with FLEX parameters
43 - charges File with charges (needed only for FLEX)
44 - tes.dat File with tesselation points needed for approximating
45 the solvent accessible surface area of atoms
46- doc A sub-directory containing:
47 - manual.pdf The manual in PDF-format describing the details
48 of various subroutines and installation of SMMP
49 - license.txt Ascii-file with the license agreement
50 - angle_defs.svg Scalable vector graphic of definition of angles
51 - atom_numbering.svg Scalable vector graphic of numbering of atoms
52 - dihedral_defs.svg Scalable vector graphic of definition of dihedrals
53 - Makefile Makefile to build documentation
54 - manual.lyx Original source of manual
55 - manual.tex Lyx file converted to tex suitable for pdflatex
56
57- Makefile Produces the executable file
58
59- INCL.H Defines global parameters and common-blocks
60- INCP.H Defines parameters and common-blocks necessary for reading
61 PDB-structures
62- incl_lund.h Defines parameters and common blocks used with the Lund
63 force field and BGS
64
65- init_molecule.f Wrapping function that constructs the start configuration
66 of a molecule
67- init_energy.f Wrapping function that initializes energy parameter
68- redseq.f Reads sequence of amino acids (e.g. enkefa.seq)
69- redvar.f Reads initial configuration of molecule (e.g. enkefa.var)
70- getmol.f Assembles data from libraries
71- bldmol.f Builds up the protein atomic coordinates
72- addend.f Adds end-groups
73- setmvs.f Determines sets of moving atoms for given variables
74- mklist.f Compiles lists of interaction partners
75- setvar.f Resets variables and rebuilds the molecule
76- dihedr.f Returns dihedral angles and valence angles
77- difang.f Calculates the difference and the sum of two angles
78- nursvr.f Calculates the residue index of a dihedral angle or atom
79- redstr.f String input routines
80- pdbread.f Reads amino acid sequence and rotein atomic coordinates from
81 a PDB-file, calculates dihedral angles from PDB coordinates,
82 and builds index field that relates PDB-atoms to SMMP atoms
83
84- energy.f Wrapping function that returns the energy of a current
85 protein configuration
86- enyflx.f Calculates internal energy of molecule with FLEX dataset
87- enyshe.f Calculates internal energy of molecule with ECEPP datasets
88- enyshe_p.f Parallel version of enyshe.f
89- enylun.f Calculates energy of molecule using the Lund force field
90- enysol.f Calculates solvation energy of molecule using solvent
91 accessible area method (fast, but approximate calculation)
92- enysol_p.f Parallel version of enysol.f
93- esolan.f Calculates solvation energy of molecule using solvent
94 accessible area method (analytic, but slow calculation)
95- eninteract.f Calculates interaction term for multi-molecule simulations
96 based on ECEPP.
97- enyreg.f Calculates a constraint energy needed for regularizing
98 PDB-structures
99- eyabgs.f Calculates correction term introduced by R. A. Abagyan
100 et al.
101
102- gradient.f Wrapping function that returns the energy gradient vs.
103 dihedral angles for a protein configuration
104- opeflx.f Calculates internal energy and partial derivatives vs.
105 dihedral angles for FLEX dataset
106- opeshe.f Calculates internal energy and partial derivatives vs.
107 dihedral angles for ECEPP datasets
108- opesol.f Calculates analytically the partial derivatives vs.
109 dihedral angles of the solvation energy
110- opereg.f Calculates the partial derivatives vs. diheadral angles
111 of the constraint energy term during regularization
112
113
114- main.f Main program
115- regul.f Regularization of PDB-structure into SMMP geometry
116- anneal.f For simulated annealing run
117- canon.f For canonical Monte Carlo run
118- minim.f For minimization of protein potential energy
119- mulcan_par.f Calculates multicanonical weights
120- mulcan_sim.f For multicanonical simulation run
121- mulcan_par_mod.f90 Combines the previous two files in a Fortran module.
122- partem_s.f For parallel tempering run on a single-processor machine
123- partem_p.f For parallel tempering run on a multiple-processor machine
124- main_p.f Replaces `main.f' on multiple-processor machine in
125 parallel tempering runs.
126- main_bgl_p.f Version of main_p.f optimized for use with IBM BlueGene/L
127
128- metropolis.f Performs Metropolis updates
129- bgs.f Biased Gaussian step.
130- minqsn.f Minimization by quasi-Newton method using BFGS-formula
131- mincjg.f Minimization by conjugate gradient method
132- outvar.f Output of the current conformation (dihedral angles)
133- contacts.f Calculates van der Waals contacts
134- cnteny.f Calculates atomic contact energy and prints bad contacts
135- hbond.f Calculates number of hydrogen bonds in a configuration
136- helix.f Measures the number of residues which are part of helix or
137 beta-sheet
138- outpdb.f Output of current configuartion in PDB-format
139- rgyr.f Measures the radius-of-gyration and end-to-end distance in
140 molecule
141- zimmer.f Expresses given configuration in Zimmerman code
142- rmsdfun.f Calculates root-mean-square deviation between current
143 SMMP configuration and a reference structure.
144
145- twister.f Mersenne-Twister random number generator
146- utilties.f Somer helper function for simulations on multiple processors.
147
148- smmp.pyf Interface of the Python bindings
149
150- universe.py Python package that provides access to global properties
151 of the system.
152- protein.py Python package representing atoms, amino acids, and proteins
153- algorithms.py Some basic algorithms using the Python bindings.
154- main.py Main program in Python
155
156- rmexclpoint.py Utility script to build the Python binding
157- restoreexclpoint.py Utility script to build the Python binding
158
159- temperatures Sample temperature file with 32 temperatures.
160
161- EXAMPLES A sub-directory containing:
162 - enkefa.seq Example sequence file
163 - enkefa.var Example configuration file
164 - enkefa.ann Example configuration filea for simulated annealing run
165 - enkefa.ref Example contact matrix file
166 - abeta.seq Sequence file for Abeta_16-22
167 - abeta.var Configuration file with global coordinates
168 - abeta.ref Dummy contact matrix
169 - 1bdd.pdb PDB file of protein A for regularization.
170 - 1bdd.ref Contact matrix of protein A
171 - 1bdd.seq Sequence file of protein A
172 - 1bdd.var Sampe configuration of protein A
173 - temperatures Example temperature file for parallel_tempering_s
174 - temperatures_abeta Example temperature file for parallel_tempering
175 - smmp.cmd Example shell-script to run smmp
176
177 - Makefile Makefile for building the examples.
178
179 - annealing.f Example for running simulated annealing
180 - minimization.f Example for a minimization
181 - multicanonical.f Example for calculating parameters for a multi canonical
182 simulation.
183 - parallel_tempering_p.f Example for parallel tempering on a cluster
184 - parallel_tempering_s.f Example for parallel tempering on a single node
185 - partem_p.f Parallel tempering routine used with parallel_tempering_p.f
186 The output is different from the default implementation.
187 - regularization.f Example for regularizing protein A (1bdd)
188
189 - Python A sub-directory containing some examples that use the Python
190 bindings.
191
192 - annealing.py Python version of the annealing example
193 - minimization.py Python version of the minimization example
194 - muca.py Python version for calculating the parameters for a
195 multi-canonical simulation.
196 - regularization.py Python version of regularization example
197 - gui_example.py Example for building a graphical user interface for SMMP
198 - best.pml A PyMol script for rendering best.pdb
199
200 - scripts A sub-directory containing some useful scripts:
201 - README Short description of the scripts
202 - atomprops.py Lists the properties of all atoms in a protein
203 - var2pdb.py Takes a sequence and a var file and builds a PDB from it.
204
205The whole SMMP package is written in standard FORTRAN language.
206We have been exploiting it under pgif, ifort, gfortran, and xlf.
207It should be possible to compile the code with any contemporary fortran
208compilers. There are no machine dependent routines included in SMMP.
209Common blocks and limiting parameters are gathered in special files
210``INCL.H'' and ``INCP.H'' which are attached to the modules through
211an `include' statement. In order to install SMMP the user needs to edit the
212`Makefile' and specify the compiler and compiler options which he will use.
213Executing the `make' command will finish installation of SMMP. For compiling
214the parallel version use `make parallel'. The command `make doc' build the
215documentation and `make pybind' build the Python bindings if f2py is installed.
216
217
218
2193) HOW TO RUN SMMP:
220SMMP does not include an interpretor of user defined commands.
221The preparation of a simulation must be done in the 'main' module
222After changes of SMMP has to be re-compiled.
223
224Alternatively, you can use the Python bindings, which allow for interactive
225simulations.
226
227The residues which can be used with each parameter set are described in
228files `lib.sh2', 'lib.sh3' and 'lib.flx', respectively. The file 'charges'
229is needed for N- and C-terminal residues with FLEX parameters. The
230directory with these 3 files should be given in string 'libdir', which
231is assigned in module 'main' or 'pmain'.
232
233SMMP requires as input a file that specifies the sequence of residues
234in a protein. This sequence can be read either from a PDB-file (the
235standard format in which protein structures are deposited in the
236Protein Data Bank) or from a special sequence file. If the sequence
237is read from a sequence file its first line must start with a '#' and
238may (or may not) contain the name for the molecule. The residues in the
239following lines should be named as in the libraries (not case-
240sensitive). Residue names should be separated by at least one space.
241An example file ("enkefa.seq") is provided in the sub-directory EXAMPLES.
242
243The initial values for internal variables, i.e. dihedral angles for single
244bonds, can be calculated either from the atomic coordinates of the PDB-file,
245or (if the sequence is read from a sequence file) may be provided in a
246SECOND INPUT file. If this file is not given (or the name of a non-existing
247file is entered), all variables retain their values given in the libraries.
248The example file ("enkefa.var") which is provided in the subdirectory
249EXAMPLES demonstrates the syntax that has to be used:
250
251 residue(s) : variable(s) : value
252
253In the first field the RESIDUE is selected through an {\it INTEGER}
254number which marks the position of that RESIDUE in the amino acid sequence.
255The second field lists a string with the name of the VARIABLE, i.e. names
256the specific dihedral angle. The last field lists the value (a {\it REAL}
257number) for the VARIABLE and is mandatory. Missing fields are interpreted
258as 'for all'. Spaces are not significant and are ignored. Empty lines or
259or lines containing '#' are ignored. A line containing '&' assigns FIXED
260variable(s), i.e. they will be set to the given value, but will NOT be
261varied during subsequent changes of the protein configuration.
262
263
264
265The following steps summarize how to run SMMP:
266
267- Assign to the character variable 'libdir' the path to the directory
268 containing the standard amino acid residue libraries and the file 'charges'.
269
270- Select the force field and solvation model by setting the four
271 'sh2', 'epsd' and 'itysol', 'ientyp' to their appropriate values:
272 * ientyp : 0 => ECEPP2 or ECEPP3 depending on the value of sh2
273 1 => FLEX
274 2 => Lund force field
275 3 => ECEPP with Abagyan corrections
276 * sh2 =.TRUE. : ECEPP/2 potential, sh2=.FALSE.: ECEPP/3
277 (Note that the variable `flex' has to be set to .FALSE.)
278 * epsd=.TRUE. : Distant dependent epsilon(r)
279 epsd=.FALSE.: epsilon=2
280 * itysol = 0 : Gas phase;
281 itysol > 0 : approximation of protein-solvent interactions by means
282 of a solvent accessible surface area approach with
283 stochastic estimation of the accessible area.
284 itysol < 0 : same as above, but the accessible area is calculated
285 analytically (much SLOWER than itysol > 0).
286
287- Choose a N-terminal and C-terminal group by setting 'grpn' and 'grpc'
288 to approbriate values.
289
290- Choose how the initial input is read in:
291 * iabin = 0 : read from PDB-file
292 * iabin = 1 : read from sequence (and configuration) file
293
294- Enter the names of the corresponding file(s). In the example
295 version of the 'main' module this is done through interactive dialog
296 but the user can easily just assign the corresponding names to the
297 character variables 'seqfil' and 'varfil' in the subroutine
298 'init_molecule'.
299
300- At this point the program is ready for calling the simulation
301 subroutines. In the provided version the energy minimization
302 subroutine is called through 'call minim'. A detailed description
303 of this and other simulation subroutines can be found in the
304 manual (file manual.ps). Normally the simulation subroutines
305 write data in output files, but one can also put output routines
306 such as `outpdb' in 'main'. The minimal output (written into
307 standard output) is the name of the sequence file (extension .seq),
308 name of configuration file (extension .var), and for each residue
309 a list of dihedral angles together with their initial values.
310
311- For parallel tempering jobs on on a multiprocessor system one has
312 to replace 'main' by 'main_p'. The above protocol still applies.
313
314
3154) LIMITATIONS:
316All parameters which limit the usage of SMMP are stored in the
317file ``INCL.H''. The most important ones are listed below.
318
319mxml=10 max. number of molecules
320mxrs=500 max. total number of residues
321mxat=10000 max. total number of atoms
322mxbd=3 max. number of bonds to following atoms
323mxvr=mxrs*5 max. number of local variables
324mxms=mxvr*3 max. total number of moving sets
325mxvw=mxat*4 max. number of vwd domains
326mx14=mxat*4 max. number of '1-4' partners
327mxath = 100 max. number of atoms in help-arrays
328mxvrh=mxath max. number of variables in help
329mxtyat=18 max. number of energetic atom-types
330mxhbdo=4 max. types of Hydrogens as donors in HB
331mxhbac=6 max. types of atoms as acceptors in HB
332mxtyto=19 max. number of types of torsional potentials
333nrsty=35 max. number of residue types
334mxtysol=9 the number of solvation parameters sets
335
336Note also the following restrictions in the current version of SMMP:
337- A single amino acid residue can not be simulated with FLEX potential.
338- A protein must not start with a prolin residue.
339
340
3415) EXAMPLE:
342Proper installation of SMMP can be tested by running the following
343example. After compilation of the program package (with `make'
344command using the provided `Makefile') and runing SMMP by typing
345./smmp, SMMP will minimize the ECEPP/3 energy of the Met-enkephalin
346configuration in `EXAMPLES/enkefa.var'.
347-----------------------------------------------------------------------
348|NOTE: If the program doesn't start but only shows the error message |
349|"Killed", you probably don't have enough memory available. You can |
350|reduce the memory requirement by setting lower limits for mxrs |
351|(line 10) and mxat (line 11) in the file INCL.H. Setting mxrs=10 and |
352|mxat=1300 will still run all the examples. |
353-----------------------------------------------------------------------
354Running the program leads to the following output:
355
356------------------------------------------------------------ enkefa.out
357
358 file with SEQUENCE:
359 ./EXAMPLES/enkefa.seq
360
361 file with VARIABLES: ./EXAMPLES/enkefa.var
362
363 redvar> Met-Enkephalin: residue 1 Tyr : x1 set -172.590
364 redvar> Met-Enkephalin: residue 1 Tyr : x2 set 78.710
365 redvar> Met-Enkephalin: residue 1 Tyr : x6 set -165.880
366 redvar> Met-Enkephalin: residue 1 Tyr : phi set -86.240
367 redvar> Met-Enkephalin: residue 2 Gly : psi set 156.180
368 redvar> Met-Enkephalin: residue 2 Gly : omg set -180.000
369 redvar> Met-Enkephalin: residue 2 Gly : phi set -154.530
370 redvar> Met-Enkephalin: residue 3 Gly : psi set 83.640
371 redvar> Met-Enkephalin: residue 3 Gly : omg set 180.000
372 redvar> Met-Enkephalin: residue 3 Gly : phi set 83.660
373 redvar> Met-Enkephalin: residue 4 Phe : psi set -73.860
374 redvar> Met-Enkephalin: residue 4 Phe : omg set -180.000
375 redvar> Met-Enkephalin: residue 4 Phe : x1 set 58.790
376 redvar> Met-Enkephalin: residue 4 Phe : x2 set 94.600
377 redvar> Met-Enkephalin: residue 4 Phe : phi set -137.040
378 redvar> Met-Enkephalin: residue 5 Met : psi set 19.330
379 redvar> Met-Enkephalin: residue 5 Met : omg set -180.000
380 redvar> Met-Enkephalin: residue 5 Met : x1 set 52.760
381 redvar> Met-Enkephalin: residue 5 Met : x2 set 175.280
382 redvar> Met-Enkephalin: residue 5 Met : x3 set -179.830
383 redvar> Met-Enkephalin: residue 5 Met : x4 set -58.570
384 redvar> Met-Enkephalin: residue 5 Met : phi set -163.630
385 redvar> Met-Enkephalin: residue 5 Met : pst set 160.450
386 redvar> Met-Enkephalin: residue 5 Met : omt set 180.000
387
388
389 Energy BEFORE minimization:
390
391 Total: 0.10354E+04
392 Coulomb: 0.1991E+02 Lennard-Jones: 0.1142E+03 HB: 0.9008E+03
393 Variables: 0.4511E+00 Solvatation: 0.0000E+00
394
395 Step 1: energy 0.489976E+05 ( 0.867243E+13 )
396 Step 2: energy 0.108241E+03 ( 0.964364E+07 )
397 Step 3: energy -0.632755E+00 ( 0.498256E+04 )
398 Step 4: energy -0.739539E+01 ( 0.109979E+05 )
399 Step 5: energy 0.517957E+03 ( 0.678892E+09 )
400 Step 6: energy -0.767774E+01 ( 0.143880E+05 )
401 Step 7: energy -0.818570E+01 ( 0.100364E+05 )
402 Step 8: energy -0.938401E+01 ( 0.172508E+04 )
403 Step 9: energy -0.109799E+02 ( 0.105718E+04 )
404 Step 10: energy -0.116244E+02 ( 0.580821E+03 )
405 Step 11: energy -0.116969E+02 ( 0.145676E+04 )
406 Step 12: energy -0.118569E+02 ( 0.856882E+03 )
407 Step 13: energy -0.119576E+02 ( 0.521381E+03 )
408 Step 14: energy -0.120897E+02 ( 0.398602E+03 )
409 Step 15: energy -0.121476E+02 ( 0.222201E+03 )
410 Step 16: energy -0.121804E+02 ( 0.242613E+03 )
411 Step 17: energy -0.121975E+02 ( 0.237765E+03 )
412 Step 18: energy -0.122092E+02 ( 0.217435E+03 )
413 Step 19: energy -0.122177E+02 ( 0.198576E+03 )
414 Step 20: energy -0.122259E+02 ( 0.181726E+03 )
415 Step 21: energy -0.122298E+02 ( 0.178796E+03 )
416 Step 22: energy -0.122318E+02 ( 0.178968E+03 )
417 Step 23: energy -0.122352E+02 ( 0.181503E+03 )
418 Step 24: energy -0.122407E+02 ( 0.184272E+03 )
419 Step 25: energy -0.122499E+02 ( 0.186336E+03 )
420 Step 26: energy -0.122634E+02 ( 0.183760E+03 )
421 Step 27: energy -0.122776E+02 ( 0.171223E+03 )
422 Step 28: energy -0.122929E+02 ( 0.148718E+03 )
423 Step 29: energy -0.123122E+02 ( 0.119336E+03 )
424 Step 30: energy -0.123348E+02 ( 0.847677E+02 )
425 Step 31: energy -0.123572E+02 ( 0.434069E+02 )
426 Step 32: energy -0.123733E+02 ( 0.176053E+02 )
427 Step 33: energy -0.123858E+02 ( 0.941361E+01 )
428 Step 34: energy -0.123956E+02 ( 0.739923E+01 )
429 Step 35: energy -0.124014E+02 ( 0.513793E+01 )
430 Step 36: energy -0.124049E+02 ( 0.385630E+01 )
431 Step 37: energy -0.124083E+02 ( 0.416421E+01 )
432 Step 38: energy -0.124122E+02 ( 0.530410E+01 )
433 Step 39: energy -0.124159E+02 ( 0.493920E+01 )
434 Step 40: energy -0.124184E+02 ( 0.306992E+01 )
435 Step 41: energy -0.124201E+02 ( 0.174747E+01 )
436 Step 42: energy -0.124216E+02 ( 0.110719E+01 )
437 Step 43: energy -0.124231E+02 ( 0.793785E+00 )
438 Step 44: energy -0.124242E+02 ( 0.585080E+00 )
439 Step 45: energy -0.124249E+02 ( 0.454481E+00 )
440 Step 46: energy -0.124257E+02 ( 0.491193E+00 )
441 Step 47: energy -0.124268E+02 ( 0.498392E+00 )
442 Step 48: energy -0.124277E+02 ( 0.297774E+00 )
443 Step 49: energy -0.124281E+02 ( 0.987143E-01 )
444 Step 50: energy -0.124282E+02 ( 0.562089E-01 )
445 Step 51: energy -0.124283E+02 ( 0.472681E-01 )
446 Step 52: energy -0.124283E+02 ( 0.360471E-01 )
447 Step 53: energy -0.124284E+02 ( 0.149691E-01 )
448 Step 54: energy -0.124285E+02 ( 0.376934E-02 )
449 Step 55: energy -0.124285E+02 ( 0.243872E-02 )
450 Step 56: energy -0.124285E+02 ( 0.253572E-02 )
451 Step 57: energy -0.124285E+02 ( 0.176076E-02 )
452 Step 58: energy -0.124285E+02 ( 0.952400E-03 )
453 Step 59: energy -0.124285E+02 ( 0.889573E-03 )
454 Step 60: energy -0.124285E+02 ( 0.747233E-03 )
455 Step 61: energy -0.124285E+02 ( 0.417036E-03 )
456 Step 62: energy -0.124285E+02 ( 0.307630E-03 )
457 Step 63: energy -0.124285E+02 ( 0.474529E-03 )
458 Step 64: energy -0.124285E+02 ( 0.506211E-03 )
459 Step 65: energy -0.124285E+02 ( 0.298789E-03 )
460 Step 66: energy -0.124285E+02 ( 0.125304E-03 )
461 Step 67: energy -0.124285E+02 ( 0.153436E-03 )
462 Step 68: energy -0.124285E+02 ( 0.132386E-03 )
463 Step 69: energy -0.124285E+02 ( 0.661655E-04 )
464 Step 70: energy -0.124285E+02 ( 0.194869E-04 )
465 Step 71: energy -0.124285E+02 ( 0.120524E-04 )
466 Step 72: energy -0.124285E+02 ( 0.641640E-05 )
467 Step 73: energy -0.124285E+02 ( 0.182141E-05 )
468 Step 74: energy -0.124285E+02 ( 0.219308E-05 )
469 Step 75: energy -0.124285E+02 ( 0.348349E-05 )
470 Step 76: energy -0.124285E+02 ( 0.166901E-05 )
471 Step 77: energy -0.124285E+02 ( 0.177102E-06 )
472 Step 78: energy -0.124285E+02 ( 0.663522E-08 )
473 Step 79: energy -0.124285E+02 ( 0.210693E-08 )
474 Step 80: energy -0.124285E+02 ( 0.370905E-08 )
475 Step 81: energy -0.124285E+02 ( 0.324300E-08 )
476 Step 82: energy -0.124285E+02 ( 0.777363E-09 )
477 Step 83: energy -0.124285E+02 ( 0.443359E-10 )
478 Step 84: energy -0.124285E+02 ( 0.322695E-11 )
479 Step 85: energy -0.124285E+02 ( 0.443359E-10 )
480 ---- CONVERGENCE ----
481
482 Final energies __________________________________________________
483
484 Total: -0.12429E+02
485 Coulomb: 0.2143E+02 Lennard-Jones: -0.2923E+02 HB: -0.6706E+01
486 Variables: 0.2084E+01 Solvatation: 0.0000E+00
487
488 Variables _________________
489
490 x1 1 -173.2 ( 0.6)
491 x2 1 79.3 ( 0.6)
492 x6 1 -166.3 ( 0.5)
493 phi 1 -83.1 ( 3.2)
494 psi 2 155.8 ( 0.4)
495 omg 2 -177.1 ( 2.9)
496 phi 2 -154.2 ( 0.3)
497 psi 3 85.8 ( 2.2)
498 omg 3 168.5 ( 11.5)
499 phi 3 83.0 ( 0.7)
500 psi 4 -75.0 ( 1.2)
501 omg 4 -170.0 ( 10.0)
502 x1 4 58.9 ( 0.1)
503 x2 4 94.5 ( 0.1)
504 phi 4 -136.8 ( 0.2)
505 psi 5 19.1 ( 0.2)
506 omg 5 -174.1 ( 5.9)
507 x1 5 52.9 ( 0.1)
508 x2 5 175.3 ( 0.0)
509 x3 5 -179.9 ( 0.0)
510 x4 5 -58.6 ( 0.0)
511 phi 5 -163.4 ( 0.2)
512 pst 5 160.8 ( 0.3)
513 omt 5 -179.8 ( 0.2)
514
515 Gradient ______________________________________________________________
516 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
517 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
518 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
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