Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2016-2020 The plumed team
3 : (see the PEOPLE file at the root of the distribution for a list of names)
4 :
5 : See http://www.plumed.org for more information.
6 :
7 : This file is part of plumed, version 2.
8 :
9 : plumed is free software: you can redistribute it and/or modify
10 : it under the terms of the GNU Lesser General Public License as published by
11 : the Free Software Foundation, either version 3 of the License, or
12 : (at your option) any later version.
13 :
14 : plumed is distributed in the hope that it will be useful,
15 : but WITHOUT ANY WARRANTY; without even the implied warranty of
16 : MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17 : GNU Lesser General Public License for more details.
18 :
19 : You should have received a copy of the GNU Lesser General Public License
20 : along with plumed. If not, see <http://www.gnu.org/licenses/>.
21 : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
22 :
23 : /* This class was originally written by Thomas Loehr */
24 :
25 : #include "Colvar.h"
26 : #include "ActionRegister.h"
27 : #include "core/ActionSet.h"
28 : #include "core/PlumedMain.h"
29 : #include "core/SetupMolInfo.h"
30 : #include "tools/OpenMP.h"
31 : #include <initializer_list>
32 :
33 : #define INV_PI_SQRT_PI 0.179587122
34 : #define KCAL_TO_KJ 4.184
35 : #define ANG_TO_NM 0.1
36 : #define ANG3_TO_NM3 0.001
37 :
38 : using namespace std;
39 :
40 : namespace PLMD {
41 : namespace colvar {
42 :
43 : //+PLUMEDOC COLVAR EEFSOLV
44 : /*
45 : Calculates EEF1 solvation free energy for a group of atoms.
46 :
47 : EEF1 is a solvent-accessible surface area based model, where the free energy of solvation is computed using a pairwise interaction term for non-hydrogen atoms:
48 : \f[
49 : \Delta G^\mathrm{solv}_i = \Delta G^\mathrm{ref}_i - \sum_{j \neq i} f_i(r_{ij}) V_j
50 : \f]
51 : where \f$\Delta G^\mathrm{solv}_i\f$ is the free energy of solvation, \f$\Delta G^\mathrm{ref}_i\f$ is the reference solvation free energy, \f$V_j\f$ is the volume of atom \f$j\f$ and
52 : \f[
53 : f_i(r) 4\pi r^2 = \frac{2}{\sqrt{\pi}} \frac{\Delta G^\mathrm{free}_i}{\lambda_i} \exp\left\{ - \frac{(r-R_i)^2}{\lambda^2_i}\right\}
54 : \f]
55 : where \f$\Delta G^\mathrm{free}_i\f$ is the solvation free energy of the isolated group, \f$\lambda_i\f$ is the correlation length equal to the width of the first solvation shell and \f$R_i\f$ is the van der Waals radius of atom \f$i\f$.
56 :
57 : The output from this collective variable, the free energy of solvation, can be used with the \ref BIASVALUE keyword to provide implicit solvation to a system. All parameters are designed to be used with a modified CHARMM36 force field. It takes only non-hydrogen atoms as input, these can be conveniently specified using the \ref GROUP action with the NDX_GROUP parameter. To speed up the calculation, EEFSOLV internally uses a neighbor list with a cutoff dependent on the type of atom (maximum of 1.95 nm). This cutoff can be extended further by using the NL_BUFFER keyword.
58 :
59 : \par Examples
60 :
61 : \plumedfile
62 : #SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb
63 : MOLINFO MOLTYPE=protein STRUCTURE=peptide.pdb
64 : WHOLEMOLECULES ENTITY0=1-111
65 :
66 : # This allows us to select only non-hydrogen atoms
67 : protein-h: GROUP NDX_FILE=index.ndx NDX_GROUP=Protein-H
68 :
69 : # We extend the cutoff by 0.2 nm and update the neighbor list every 10 steps
70 : solv: EEFSOLV ATOMS=protein-h NL_STRIDE=10 NL_BUFFER=0.2
71 :
72 : # Here we actually add our calculated energy back to the potential
73 : bias: BIASVALUE ARG=solv
74 :
75 : PRINT ARG=solv FILE=SOLV
76 : \endplumedfile
77 :
78 : */
79 : //+ENDPLUMEDOC
80 :
81 4 : class EEFSolv : public Colvar {
82 : private:
83 : bool pbc;
84 : double buffer;
85 : double delta_g_ref;
86 : unsigned stride;
87 : unsigned nl_update;
88 : vector<vector<unsigned> > nl;
89 : vector<vector<bool> > nlexpo;
90 : vector<vector<double> > parameter;
91 : void setupConstants(const vector<AtomNumber> &atoms, vector<vector<double> > ¶meter, bool tcorr);
92 : map<string, map<string, string> > setupTypeMap();
93 : map<string, vector<double> > setupValueMap();
94 : void update_neighb();
95 :
96 : public:
97 : static void registerKeywords(Keywords& keys);
98 : explicit EEFSolv(const ActionOptions&);
99 : virtual void calculate();
100 : };
101 :
102 7360 : PLUMED_REGISTER_ACTION(EEFSolv,"EEFSOLV")
103 :
104 3 : void EEFSolv::registerKeywords(Keywords& keys) {
105 3 : Colvar::registerKeywords(keys);
106 3 : componentsAreNotOptional(keys);
107 3 : useCustomisableComponents(keys);
108 12 : keys.add("atoms", "ATOMS", "The atoms to be included in the calculation, e.g. the whole protein.");
109 12 : keys.add("compulsory", "NL_BUFFER", "The buffer to the intrinsic cutoff used when calculating pairwise interactions.");
110 12 : keys.add("compulsory", "NL_STRIDE", "The frequency with which the neighbor list is updated.");
111 9 : keys.addFlag("TEMP_CORRECTION", false, "Correct free energy of solvation constants for temperatures different from 298.15 K");
112 3 : }
113 :
114 2 : EEFSolv::EEFSolv(const ActionOptions&ao):
115 : PLUMED_COLVAR_INIT(ao),
116 : pbc(true),
117 : buffer(0.1),
118 : delta_g_ref(0.),
119 : stride(10),
120 6 : nl_update(0)
121 : {
122 : vector<AtomNumber> atoms;
123 4 : parseAtomList("ATOMS", atoms);
124 : const unsigned size = atoms.size();
125 2 : bool tcorr = false;
126 4 : parseFlag("TEMP_CORRECTION", tcorr);
127 4 : parse("NL_BUFFER", buffer);
128 4 : parse("NL_STRIDE", stride);
129 :
130 2 : bool nopbc = !pbc;
131 4 : parseFlag("NOPBC", nopbc);
132 2 : pbc = !nopbc;
133 :
134 2 : checkRead();
135 :
136 6 : log << " Bibliography " << plumed.cite("Lazaridis T, Karplus M, Proteins Struct. Funct. Genet. 35, 133 (1999)"); log << "\n";
137 :
138 :
139 2 : nl.resize(size);
140 2 : nlexpo.resize(size);
141 4 : parameter.resize(size, vector<double>(4, 0));
142 2 : setupConstants(atoms, parameter, tcorr);
143 :
144 2 : addValueWithDerivatives();
145 2 : setNotPeriodic();
146 2 : requestAtoms(atoms);
147 2 : }
148 :
149 1146 : void EEFSolv::update_neighb() {
150 : const double lower_c2 = 0.24 * 0.24; // this is the cut-off for bonded atoms
151 : const unsigned size = getNumberOfAtoms();
152 138666 : for (unsigned i=0; i<size; ++i) {
153 68760 : nl[i].clear();
154 : nlexpo[i].clear();
155 137520 : const Vector posi = getPosition(i);
156 : // Loop through neighboring atoms, add the ones below cutoff
157 2097180 : for (unsigned j=i+1; j<size; ++j) {
158 4056840 : const double d2 = delta(posi, getPosition(j)).modulo2();
159 2028420 : if (d2 < lower_c2 && j < i+14) {
160 : // crude approximation for i-i+1/2 interactions,
161 : // we want to exclude atoms separated by less than three bonds
162 102949 : continue;
163 : }
164 : // We choose the maximum lambda value and use a more conservative cutoff
165 1925471 : double mlambda = 1./parameter[i][2];
166 3850942 : if (1./parameter[j][2] > mlambda) mlambda = 1./parameter[j][2];
167 1925471 : const double c2 = (4. * mlambda + buffer) * (4. * mlambda + buffer);
168 1925471 : if (d2 < c2 ) {
169 1925089 : nl[i].push_back(j);
170 3850178 : if(parameter[i][2] == parameter[j][2] && parameter[i][3] == parameter[j][3]) {
171 420964 : nlexpo[i].push_back(true);
172 1504125 : } else nlexpo[i].push_back(false);
173 : }
174 : }
175 : }
176 1146 : }
177 :
178 1146 : void EEFSolv::calculate() {
179 1146 : if(pbc) makeWhole();
180 1146 : if(getExchangeStep()) nl_update = 0;
181 1146 : if (nl_update == 0) {
182 1146 : update_neighb();
183 : }
184 :
185 : const unsigned size=getNumberOfAtoms();
186 : double bias = 0.0;
187 1146 : Tensor deriv_box;
188 1146 : unsigned nt=OpenMP::getNumThreads();
189 1146 : const unsigned nn=nl.size();
190 1146 : if(nt*10>nn) nt=1;
191 3438 : #pragma omp parallel num_threads(nt)
192 : {
193 2292 : vector<Vector> deriv_omp(size);
194 2292 : #pragma omp for reduction(+:bias)
195 : for (unsigned i=0; i<size; ++i) {
196 137520 : const Vector posi = getPosition(i);
197 : double fedensity = 0.0;
198 68760 : Vector deriv_i;
199 137520 : const double vdw_volume_i = parameter[i][0];
200 68760 : const double delta_g_free_i = parameter[i][1];
201 68760 : const double inv_lambda_i = parameter[i][2];
202 68760 : const double vdw_radius_i = parameter[i][3];
203 :
204 : // The pairwise interactions are unsymmetric, but we can get away with calculating the distance only once
205 5912787 : for (unsigned i_nl=0; i_nl<nl[i].size(); ++i_nl) {
206 1925089 : const unsigned j = nl[i][i_nl];
207 3850178 : const double vdw_volume_j = parameter[j][0];
208 1925089 : const double delta_g_free_j = parameter[j][1];
209 1925089 : const double inv_lambda_j = parameter[j][2];
210 1925089 : const double vdw_radius_j = parameter[j][3];
211 :
212 3850178 : const Vector dist = delta(posi, getPosition(j));
213 1925089 : const double rij = dist.modulo();
214 1925089 : const double inv_rij = 1.0 / rij;
215 1925089 : const double inv_rij2 = inv_rij * inv_rij;
216 1925089 : const double fact_ij = inv_rij2 * delta_g_free_i * vdw_volume_j * INV_PI_SQRT_PI* inv_lambda_i;
217 1925089 : const double fact_ji = inv_rij2 * delta_g_free_j * vdw_volume_i * INV_PI_SQRT_PI* inv_lambda_j;
218 : double deriv = 0.;
219 :
220 : // in this case we can calculate a single exponential
221 1925089 : if(!nlexpo[i][i_nl]) {
222 : // i-j interaction
223 1504125 : if(inv_rij > 0.25*inv_lambda_i)
224 : {
225 1457521 : const double inv_lambda2_i = inv_lambda_i * inv_lambda_i;
226 1457521 : const double rij_vdwr_diff = rij - vdw_radius_i;
227 1457521 : const double expo = exp(-inv_lambda2_i * rij_vdwr_diff * rij_vdwr_diff);
228 1457521 : const double fact = expo * fact_ij;
229 1457521 : fedensity += fact;
230 1457521 : deriv += inv_rij * fact * (inv_rij + rij_vdwr_diff * inv_lambda2_i);
231 : }
232 :
233 : // j-i interaction
234 1504125 : if(inv_rij > 0.25*inv_lambda_j)
235 : {
236 1419703 : const double inv_lambda2_j = inv_lambda_j * inv_lambda_j;
237 1419703 : const double rij_vdwr_diff = rij - vdw_radius_j;
238 1419703 : const double expo = exp(-inv_lambda2_j * rij_vdwr_diff * rij_vdwr_diff);
239 1419703 : const double fact = expo * fact_ji;
240 1419703 : fedensity += fact;
241 1419703 : deriv += inv_rij * fact * (inv_rij + rij_vdwr_diff * inv_lambda2_j);
242 : }
243 : } else {
244 : // i-j interaction
245 420964 : if(inv_rij > 0.25*inv_lambda_i)
246 : {
247 417717 : const double inv_lambda2 = inv_lambda_i * inv_lambda_i;
248 417717 : const double rij_vdwr_diff = rij - vdw_radius_i;
249 417717 : const double expo = exp(-inv_lambda2 * rij_vdwr_diff * rij_vdwr_diff);
250 417717 : const double fact = expo*(fact_ij + fact_ji);
251 417717 : fedensity += fact;
252 417717 : deriv += inv_rij * fact * (inv_rij + rij_vdwr_diff * inv_lambda2);
253 : }
254 : }
255 :
256 1925089 : const Vector dd = deriv*dist;
257 1925089 : deriv_i += dd;
258 1925089 : deriv_omp[j] -= dd;
259 : }
260 68760 : deriv_omp[i] += deriv_i;
261 68760 : bias += - 0.5 * fedensity;
262 : }
263 4584 : #pragma omp critical
264 277332 : for(unsigned i=0; i<size; i++) {
265 412560 : setAtomsDerivatives(i, -deriv_omp[i]);
266 275040 : deriv_box += Tensor(getPosition(i), -deriv_omp[i]);
267 : }
268 : }
269 :
270 2292 : setBoxDerivatives(-deriv_box);
271 1146 : setValue(delta_g_ref + bias);
272 :
273 : // Keep track of the neighbourlist updates
274 1146 : ++nl_update;
275 1146 : if (nl_update == stride) {
276 1146 : nl_update = 0;
277 : }
278 1146 : }
279 :
280 2 : void EEFSolv::setupConstants(const vector<AtomNumber> &atoms, vector<vector<double> > ¶meter, bool tcorr) {
281 2 : vector<vector<double> > parameter_temp;
282 2 : parameter_temp.resize(atoms.size());
283 : map<string, vector<double> > valuemap;
284 : map<string, map<string, string> > typemap;
285 4 : valuemap = setupValueMap();
286 4 : typemap = setupTypeMap();
287 4 : vector<SetupMolInfo*> moldat = plumed.getActionSet().select<SetupMolInfo*>();
288 : bool cter=false;
289 2 : if (moldat.size() == 1) {
290 2 : log << " MOLINFO DATA found, using proper atom names\n";
291 364 : for(unsigned i=0; i<atoms.size(); ++i) {
292 :
293 : // Get atom and residue names
294 240 : string Aname = moldat[0]->getAtomName(atoms[i]);
295 240 : string Rname = moldat[0]->getResidueName(atoms[i]);
296 120 : string Atype = typemap[Rname][Aname];
297 :
298 : // Check for terminal COOH or COO- (different atomtypes & parameters!)
299 960 : if (moldat[0]->getAtomName(atoms[i]) == "OT1" || moldat[0]->getAtomName(atoms[i]) == "OXT") {
300 : // We create a temporary AtomNumber object to access future atoms
301 : unsigned ai = atoms[i].index();
302 : AtomNumber tmp_an;
303 0 : tmp_an.setIndex(ai + 2);
304 0 : if (moldat[0]->getAtomName(tmp_an) == "HT2") {
305 : // COOH
306 : Atype = "OB";
307 : } else {
308 : // COO-
309 : Atype = "OC";
310 : }
311 : cter = true;
312 : }
313 600 : if (moldat[0]->getAtomName(atoms[i]) == "OT2" || (cter == true && moldat[0]->getAtomName(atoms[i]) == "O")) {
314 : unsigned ai = atoms[i].index();
315 : AtomNumber tmp_an;
316 0 : tmp_an.setIndex(ai + 1);
317 0 : if (moldat[0]->getAtomName(tmp_an) == "HT2") {
318 : // COOH
319 : Atype = "OH1";
320 : } else {
321 : // COO-
322 : Atype = "OC";
323 : }
324 : }
325 :
326 : // Check for H-atoms
327 : char type;
328 120 : char first = Aname.at(0);
329 :
330 : // GOLDEN RULE: type is first letter, if not a number
331 120 : if (!isdigit(first)) {
332 : type = first;
333 : // otherwise is the second
334 : } else {
335 0 : type = Aname.at(1);
336 : }
337 :
338 120 : if (type == 'H') {
339 0 : error("EEF1-SB does not allow the use of hydrogen atoms!\n");
340 : }
341 :
342 : // Lookup atomtype in table or throw exception if its not there
343 : try {
344 240 : parameter_temp[i] = valuemap.at(Atype);
345 0 : } catch (exception &e) {
346 0 : log << "Type: " << Atype << " Name: " << Aname << " Residue: " << Rname << "\n";
347 0 : error("Invalid atom type!\n");
348 : }
349 :
350 : // Temperature correction
351 120 : if (tcorr && parameter[i][1] > 0.0) {
352 : const double t0 = 298.15;
353 0 : const double delta_g_ref_t0 = parameter_temp[i][1];
354 0 : const double delta_h_ref_t0 = parameter_temp[i][3];
355 0 : const double delta_cp = parameter_temp[i][4];
356 0 : const double delta_s_ref_t0 = (delta_h_ref_t0 - delta_g_ref_t0) / t0;
357 0 : const double t = plumed.getAtoms().getKbT() / plumed.getAtoms().getKBoltzmann();
358 0 : parameter_temp[i][1] -= delta_s_ref_t0 * (t - t0) - delta_cp * t * std::log(t / t0) + delta_cp * (t - t0);
359 0 : parameter_temp[i][2] *= parameter_temp[i][1] / delta_g_ref_t0;
360 : }
361 120 : parameter[i][0] = parameter_temp[i][0];
362 120 : parameter[i][1] = parameter_temp[i][2];
363 120 : parameter[i][2] = parameter_temp[i][5];
364 120 : parameter[i][3] = parameter_temp[i][6];
365 : }
366 : } else {
367 0 : error("MOLINFO DATA not found\n");
368 : }
369 364 : for(unsigned i=0; i<atoms.size(); ++i) delta_g_ref += parameter_temp[i][1];
370 2 : }
371 :
372 2 : map<string, map<string, string> > EEFSolv::setupTypeMap() {
373 : map<string, map<string, string> > typemap;
374 1000 : typemap = {
375 : { "ACE", {
376 : {"CH3", "CT3"},
377 : {"HH31","HA3"},
378 : {"HH32","HA3"},
379 : {"HH33","HA3"},
380 : {"C", "C" },
381 : {"O", "O" }
382 : }
383 : },
384 : { "ALA", {
385 : {"N", "NH1"},
386 : {"HN", "H" },
387 : {"CA", "CT1"},
388 : {"HA", "HB1"},
389 : {"CB", "CT3"},
390 : {"HB1", "HA3"},
391 : {"HB2", "HA3"},
392 : {"HB3", "HA3"},
393 : {"C", "C" },
394 : {"O", "O" }
395 : }
396 : },
397 : { "ARG", {
398 : {"N", "NH1"},
399 : {"HN", "H" },
400 : {"CA", "CT1"},
401 : {"HA", "HB1"},
402 : {"CB", "CT2"},
403 : {"HB1", "HA2"},
404 : {"HB2", "HA2"},
405 : {"CG", "CT2"},
406 : {"HG1", "HA2"},
407 : {"HG2", "HA2"},
408 : {"CD", "CT2"},
409 : {"HD1", "HA2"},
410 : {"HD2", "HA2"},
411 : {"NE", "NC2"},
412 : {"HE", "HC" },
413 : {"CZ", "C" },
414 : {"NH1", "NC2"},
415 : {"HH11", "HC" },
416 : {"HH12", "HC" },
417 : {"NH2", "NC2"},
418 : {"HH21", "HC" },
419 : {"HH22", "HC" },
420 : {"C", "C" },
421 : {"O", "O" }
422 : }
423 : },
424 : { "ASN", {
425 : {"N", "NH1"},
426 : {"HN", "H" },
427 : {"CA", "CT1"},
428 : {"HA", "HB1"},
429 : {"CB", "CT2"},
430 : {"HB1", "HA2"},
431 : {"HB2", "HA2"},
432 : {"CG", "CC" },
433 : {"OD1", "O" },
434 : {"ND2", "NH2"},
435 : {"HD21", "H" },
436 : {"HD22", "H" },
437 : {"C", "C" },
438 : {"O", "O" }
439 : }
440 : },
441 : { "ASPP", {
442 : {"N", "NH1"},
443 : {"HN", "H" },
444 : {"CA", "CT1"},
445 : {"HA", "HB1"},
446 : {"CB", "CT2"},
447 : {"HB1", "HA2"},
448 : {"HB2", "HA2"},
449 : {"CG", "CD" },
450 : {"OD1", "OB" },
451 : {"OD2", "OH1"},
452 : {"HD2", "H" },
453 : {"C", "C" },
454 : {"O", "O" }
455 : }
456 : },
457 : { "ASP", {
458 : {"N", "NH1"},
459 : {"HN", "H" },
460 : {"CA", "CT1"},
461 : {"HA", "HB1"},
462 : {"CB", "CT2"},
463 : {"HB1", "HA2"},
464 : {"HB2", "HA2"},
465 : {"CG", "CC" },
466 : {"OD1", "OC" },
467 : {"OD2", "OC" },
468 : {"C", "C" },
469 : {"O", "O" }
470 : }
471 : },
472 : { "CYS", {
473 : {"N", "NH1"},
474 : {"HN", "H" },
475 : {"CA", "CT1"},
476 : {"HA", "HB1"},
477 : {"CB", "CT2"},
478 : {"HB1", "HA2"},
479 : {"HB2", "HA2"},
480 : {"SG", "S" },
481 : {"HG1", "HS" },
482 : {"C", "C" },
483 : {"O", "O" }
484 : }
485 : },
486 : { "GLN", {
487 : {"N", "NH1" },
488 : {"HN", "H" },
489 : {"CA", "CT1" },
490 : {"HA", "HB1" },
491 : {"CB", "CT2" },
492 : {"HB1", "HA2" },
493 : {"HB2", "HA2" },
494 : {"CG", "CT2" },
495 : {"HG1", "HA2" },
496 : {"HG2", "HA2" },
497 : {"CD", "CC" },
498 : {"OE1", "O" },
499 : {"NE2", "NH2" },
500 : {"HE21", "H" },
501 : {"HE22", "H" },
502 : {"C", "C" },
503 : {"O", "O" }
504 : }
505 : },
506 : { "GLUP", {
507 : {"N", "NH1"},
508 : {"HN", "H" },
509 : {"CA", "CT1"},
510 : {"HA", "HB1"},
511 : {"CB", "CT2"},
512 : {"HB1", "HA2"},
513 : {"HB2", "HA2"},
514 : {"CG", "CT2"},
515 : {"HG1", "HA2"},
516 : {"HG2", "HA2"},
517 : {"CD", "CD" },
518 : {"OE1", "OB" },
519 : {"OE2", "OH1"},
520 : {"HE2", "H" },
521 : {"C", "C" },
522 : {"O", "O" }
523 : }
524 : },
525 : { "GLU", {
526 : {"N", "NH1"},
527 : {"HN", "H" },
528 : {"CA", "CT1"},
529 : {"HA", "HB1"},
530 : {"CB", "CT2"},
531 : {"HB1", "HA2"},
532 : {"HB2", "HA2"},
533 : {"CG", "CT2"},
534 : {"HG1", "HA2"},
535 : {"HG2", "HA2"},
536 : {"CD", "CC" },
537 : {"OE1", "OC" },
538 : {"OE2", "OC" },
539 : {"C", "C" },
540 : {"O", "O" }
541 : }
542 : },
543 : { "GLY", {
544 : {"N", "NH1"},
545 : {"HN", "H" },
546 : {"CA", "CT2"},
547 : {"HA1", "HB2"},
548 : {"HA2", "HB2"},
549 : {"C", "C" },
550 : {"O", "O" }
551 : }
552 : },
553 : { "HSD", {
554 : {"N", "NH1"},
555 : {"HN", "H" },
556 : {"CA", "CT1"},
557 : {"HA", "HB1"},
558 : {"CB", "CT2"},
559 : {"HB1", "HA2"},
560 : {"HB2", "HA2"},
561 : {"ND1", "NR1"},
562 : {"HD1", "H" },
563 : {"CG", "CPH1"},
564 : {"CE1", "CPH2"},
565 : {"HE1", "HR1"},
566 : {"NE2", "NR2"},
567 : {"CD2", "CPH1"},
568 : {"HD2", "HR3"},
569 : {"C", "C" },
570 : {"O", "O" }
571 : }
572 : },
573 : { "HIS", {
574 : {"N", "NH1"},
575 : {"HN", "H" },
576 : {"CA", "CT1"},
577 : {"HA", "HB1"},
578 : {"CB", "CT2"},
579 : {"HB1", "HA2"},
580 : {"HB2", "HA2"},
581 : {"ND1", "NR2"},
582 : {"CG", "CPH1"},
583 : {"CE1", "CPH2"},
584 : {"HE1", "HR1"},
585 : {"NE2", "NR1"},
586 : {"HE2", "H" },
587 : {"CD2", "CPH1"},
588 : {"HD2", "HR3"},
589 : {"C", "C" },
590 : {"O", "O" }
591 : }
592 : },
593 : { "HSE", {
594 : {"N", "NH1"},
595 : {"HN", "H" },
596 : {"CA", "CT1"},
597 : {"HA", "HB1"},
598 : {"CB", "CT2"},
599 : {"HB1", "HA2"},
600 : {"HB2", "HA2"},
601 : {"ND1", "NR2"},
602 : {"CG", "CPH1"},
603 : {"CE1", "CPH2"},
604 : {"HE1", "HR1"},
605 : {"NE2", "NR1"},
606 : {"HE2", "H" },
607 : {"CD2", "CPH1"},
608 : {"HD2", "HR3"},
609 : {"C", "C" },
610 : {"O", "O" }
611 : }
612 : },
613 : { "HSP", {
614 : {"N", "NH1"},
615 : {"HN", "H" },
616 : {"CA", "CT1"},
617 : {"HA", "HB1"},
618 : {"CB", "CT2"},
619 : {"HB1", "HA2"},
620 : {"HB2", "HA2"},
621 : {"CD2", "CPH1"},
622 : {"HD2", "HR1"},
623 : {"CG", "CPH1"},
624 : {"NE2", "NR3"},
625 : {"HE2", "H" },
626 : {"ND1", "NR3"},
627 : {"HD1", "H" },
628 : {"CE1", "CPH2"},
629 : {"HE1", "HR2"},
630 : {"C", "C" },
631 : {"O", "O" }
632 : }
633 : },
634 : { "ILE", {
635 : {"N", "NH1"},
636 : {"HN", "H" },
637 : {"CA", "CT1"},
638 : {"HA", "HB1"},
639 : {"CB", "CT1"},
640 : {"HB", "HA1"},
641 : {"CG2", "CT3"},
642 : {"HG21", "HA3"},
643 : {"HG22", "HA3"},
644 : {"HG23", "HA3"},
645 : {"CG1", "CT2"},
646 : {"HG11", "HA2"},
647 : {"HG12", "HA2"},
648 : {"CD", "CT3"},
649 : {"HD1", "HA3"},
650 : {"HD2", "HA3"},
651 : {"HD3", "HA3"},
652 : {"C", "C" },
653 : {"O", "O" }
654 : }
655 : },
656 : { "LEU", {
657 : {"N", "NH1"},
658 : {"HN", "H" },
659 : {"CA", "CT1"},
660 : {"HA", "HB1"},
661 : {"CB", "CT2"},
662 : {"HB1", "HA2"},
663 : {"HB2", "HA2"},
664 : {"CG", "CT1"},
665 : {"HG", "HA1"},
666 : {"CD1", "CT3"},
667 : {"HD11", "HA3"},
668 : {"HD12", "HA3"},
669 : {"HD13", "HA3"},
670 : {"CD2", "CT3"},
671 : {"HD21", "HA3"},
672 : {"HD22", "HA3"},
673 : {"HD23", "HA3"},
674 : {"C", "C" },
675 : {"O", "O" }
676 : }
677 : },
678 : { "LYS", {
679 : {"N", "NH1"},
680 : {"HN", "H" },
681 : {"CA", "CT1"},
682 : {"HA", "HB1"},
683 : {"CB", "CT2"},
684 : {"HB1", "HA2"},
685 : {"HB2", "HA2"},
686 : {"CG", "CT2"},
687 : {"HG1", "HA2"},
688 : {"HG2", "HA2"},
689 : {"CD", "CT2"},
690 : {"HD1", "HA2"},
691 : {"HD2", "HA2"},
692 : {"CE", "CT2"},
693 : {"HE1", "HA2"},
694 : {"HE2", "HA2"},
695 : {"NZ", "NH3"},
696 : {"HZ1", "HC" },
697 : {"HZ2", "HC" },
698 : {"HZ3", "HC" },
699 : {"C", "C" },
700 : {"O", "O" }
701 : }
702 : },
703 : { "MET", {
704 : {"N", "NH1"},
705 : {"HN", "H" },
706 : {"CA", "CT1"},
707 : {"HA", "HB1"},
708 : {"CB", "CT2"},
709 : {"HB1", "HA2"},
710 : {"HB2", "HA2"},
711 : {"CG", "CT2"},
712 : {"HG1", "HA2"},
713 : {"HG2", "HA2"},
714 : {"SD", "S" },
715 : {"CE", "CT3"},
716 : {"HE1", "HA3"},
717 : {"HE2", "HA3"},
718 : {"HE3", "HA3"},
719 : {"C", "C" },
720 : {"O", "O" }
721 : }
722 : },
723 : { "NMA", {
724 : {"N", "NH1"},
725 : {"HN", "H" },
726 : {"CH3", "CT3"},
727 : {"HH31","HA3"},
728 : {"HH32","HA3"},
729 : {"HH33","HA3"},
730 : }
731 : },
732 : { "PHE", {
733 : {"N", "NH1"},
734 : {"HN", "H" },
735 : {"CA", "CT1"},
736 : {"HA", "HB1"},
737 : {"CB", "CT2"},
738 : {"HB1", "HA2"},
739 : {"HB2", "HA2"},
740 : {"CG", "CA" },
741 : {"CD1", "CA" },
742 : {"HD1", "HP" },
743 : {"CE1", "CA" },
744 : {"HE1", "HP" },
745 : {"CZ", "CA" },
746 : {"HZ", "HP" },
747 : {"CD2", "CA" },
748 : {"HD2", "HP" },
749 : {"CE2", "CA" },
750 : {"HE2", "HP" },
751 : {"C", "C" },
752 : {"O", "O" }
753 : }
754 : },
755 : { "PRO", {
756 : {"N", "N" },
757 : {"CD", "CP3"},
758 : {"HD1", "HA2"},
759 : {"HD2", "HA2"},
760 : {"CA", "CP1"},
761 : {"HA", "HB1"},
762 : {"CB", "CP2"},
763 : {"HB1", "HA2"},
764 : {"HB2", "HA2"},
765 : {"CG", "CP2"},
766 : {"HG1", "HA2"},
767 : {"HG2", "HA2"},
768 : {"C", "C" },
769 : {"O", "O" }
770 : }
771 : },
772 : { "SER", {
773 : {"N", "NH1"},
774 : {"HN", "H" },
775 : {"CA", "CT1"},
776 : {"HA", "HB1"},
777 : {"CB", "CT2"},
778 : {"HB1", "HA2"},
779 : {"HB2", "HA2"},
780 : {"OG", "OH1"},
781 : {"HG1", "H" },
782 : {"C", "C" },
783 : {"O", "O" }
784 : }
785 : },
786 : { "THR", {
787 : {"N", "NH1"},
788 : {"HN", "H" },
789 : {"CA", "CT1"},
790 : {"HA", "HB1"},
791 : {"CB", "CT1"},
792 : {"HB", "HA1"},
793 : {"OG1", "OH1"},
794 : {"HG1", "H" },
795 : {"CG2", "CT3"},
796 : {"HG21", "HA3"},
797 : {"HG22", "HA3"},
798 : {"HG23", "HA3"},
799 : {"C", "C" },
800 : {"O", "O" }
801 : }
802 : },
803 : { "TRP", {
804 : {"N", "NH1"},
805 : {"HN", "H" },
806 : {"CA", "CT1"},
807 : {"HA", "HB1"},
808 : {"CB", "CT2"},
809 : {"HB1", "HA2"},
810 : {"HB2", "HA2"},
811 : {"CG", "CY" },
812 : {"CD1", "CA" },
813 : {"HD1", "HP" },
814 : {"NE1", "NY" },
815 : {"HE1", "H" },
816 : {"CE2", "CPT"},
817 : {"CD2", "CPT"},
818 : {"CE3", "CAI"},
819 : {"HE3", "HP" },
820 : {"CZ3", "CA" },
821 : {"HZ3", "HP" },
822 : {"CZ2", "CAI"},
823 : {"HZ2", "HP" },
824 : {"CH2", "CA" },
825 : {"HH2", "HP" },
826 : {"C", "C" },
827 : {"O", "O" }
828 : }
829 : },
830 : { "TYR", {
831 : {"N", "NH1"},
832 : {"HN", "H" },
833 : {"CA", "CT1"},
834 : {"HA", "HB1"},
835 : {"CB", "CT2"},
836 : {"HB1", "HA2"},
837 : {"HB2", "HA2"},
838 : {"CG", "CA" },
839 : {"CD1", "CA" },
840 : {"HD1", "HP" },
841 : {"CE1", "CA" },
842 : {"HE1", "HP" },
843 : {"CZ", "CA" },
844 : {"OH", "OH1"},
845 : {"HH", "H" },
846 : {"CD2", "CA" },
847 : {"HD2", "HP" },
848 : {"CE2", "CA" },
849 : {"HE2", "HP" },
850 : {"C", "C" },
851 : {"O", "O" }
852 : }
853 : },
854 : { "VAL", {
855 : {"N", "NH1"},
856 : {"HN", "H" },
857 : {"CA", "CT1"},
858 : {"HA", "HB1"},
859 : {"CB", "CT1"},
860 : {"HB", "HA1"},
861 : {"CG1", "CT3"},
862 : {"HG11", "HA3"},
863 : {"HG12", "HA3"},
864 : {"HG13", "HA3"},
865 : {"CG2", "CT3"},
866 : {"HG21", "HA3"},
867 : {"HG22", "HA3"},
868 : {"HG23", "HA3"},
869 : {"C", "C" },
870 : {"O", "O" }
871 : }
872 : }
873 888 : };
874 2 : return typemap;
875 : }
876 :
877 2 : map<string, vector<double> > EEFSolv::setupValueMap() {
878 : // Volume ∆Gref ∆Gfree ∆H ∆Cp λ vdw_radius
879 : map<string, vector<double> > valuemap;
880 202 : valuemap = {
881 : { "C", {
882 : ANG3_TO_NM3 * 14.720,
883 : KCAL_TO_KJ * 0.000,
884 : KCAL_TO_KJ * 0.000,
885 : KCAL_TO_KJ * 0.000,
886 : KCAL_TO_KJ * 0.0,
887 : 1. / (ANG_TO_NM * 3.5),
888 : 0.20,
889 : }
890 : },
891 : { "CD", {
892 : ANG3_TO_NM3 * 14.720,
893 : KCAL_TO_KJ * 0.000,
894 : KCAL_TO_KJ * 0.000,
895 : KCAL_TO_KJ * 0.000,
896 : KCAL_TO_KJ * 0.0,
897 : 1. / (ANG_TO_NM * 3.5),
898 : 0.20,
899 : }
900 : },
901 : { "CT1", {
902 : ANG3_TO_NM3 * 11.507,
903 : KCAL_TO_KJ * -0.187,
904 : KCAL_TO_KJ * -0.187,
905 : KCAL_TO_KJ * 0.876,
906 : KCAL_TO_KJ * 0.0,
907 : 1. / (ANG_TO_NM * 3.5),
908 : 0.20,
909 : }
910 : },
911 : { "CT2", {
912 : ANG3_TO_NM3 * 18.850,
913 : KCAL_TO_KJ * 0.372,
914 : KCAL_TO_KJ * 0.372,
915 : KCAL_TO_KJ * -0.610,
916 : KCAL_TO_KJ * 18.6,
917 : 1. / (ANG_TO_NM * 3.5),
918 : 0.20,
919 : }
920 : },
921 : { "CT2A", {
922 : ANG3_TO_NM3 * 18.666,
923 : KCAL_TO_KJ * 0.372,
924 : KCAL_TO_KJ * 0.372,
925 : KCAL_TO_KJ * -0.610,
926 : KCAL_TO_KJ * 18.6,
927 : 1. / (ANG_TO_NM * 3.5),
928 : 0.20,
929 : }
930 : },
931 : { "CT3", {
932 : ANG3_TO_NM3 * 27.941,
933 : KCAL_TO_KJ * 1.089,
934 : KCAL_TO_KJ * 1.089,
935 : KCAL_TO_KJ * -1.779,
936 : KCAL_TO_KJ * 35.6,
937 : 1. / (ANG_TO_NM * 3.5),
938 : 0.204,
939 : }
940 : },
941 : { "CPH1", {
942 : ANG3_TO_NM3 * 5.275,
943 : KCAL_TO_KJ * 0.057,
944 : KCAL_TO_KJ * 0.080,
945 : KCAL_TO_KJ * -0.973,
946 : KCAL_TO_KJ * 6.9,
947 : 1. / (ANG_TO_NM * 3.5),
948 : 0.18,
949 : }
950 : },
951 : { "CPH2", {
952 : ANG3_TO_NM3 * 11.796,
953 : KCAL_TO_KJ * 0.057,
954 : KCAL_TO_KJ * 0.080,
955 : KCAL_TO_KJ * -0.973,
956 : KCAL_TO_KJ * 6.9,
957 : 1. / (ANG_TO_NM * 3.5),
958 : 0.18,
959 : }
960 : },
961 : { "CPT", {
962 : ANG3_TO_NM3 * 4.669,
963 : KCAL_TO_KJ * -0.890,
964 : KCAL_TO_KJ * -0.890,
965 : KCAL_TO_KJ * 2.220,
966 : KCAL_TO_KJ * 6.9,
967 : 1. / (ANG_TO_NM * 3.5),
968 : 0.186,
969 : }
970 : },
971 : { "CY", {
972 : ANG3_TO_NM3 * 10.507,
973 : KCAL_TO_KJ * -0.890,
974 : KCAL_TO_KJ * -0.890,
975 : KCAL_TO_KJ * 2.220,
976 : KCAL_TO_KJ * 6.9,
977 : 1. / (ANG_TO_NM * 3.5),
978 : 0.199,
979 : }
980 : },
981 : { "CP1", {
982 : ANG3_TO_NM3 * 25.458,
983 : KCAL_TO_KJ * -0.187,
984 : KCAL_TO_KJ * -0.187,
985 : KCAL_TO_KJ * 0.876,
986 : KCAL_TO_KJ * 0.0,
987 : 1. / (ANG_TO_NM * 3.5),
988 : 0.227,
989 : }
990 : },
991 : { "CP2", {
992 : ANG3_TO_NM3 * 19.880,
993 : KCAL_TO_KJ * 0.372,
994 : KCAL_TO_KJ * 0.372,
995 : KCAL_TO_KJ * -0.610,
996 : KCAL_TO_KJ * 18.6,
997 : 1. / (ANG_TO_NM * 3.5),
998 : 0.217,
999 : }
1000 : },
1001 : { "CP3", {
1002 : ANG3_TO_NM3 * 26.731,
1003 : KCAL_TO_KJ * 0.372,
1004 : KCAL_TO_KJ * 0.372,
1005 : KCAL_TO_KJ * -0.610,
1006 : KCAL_TO_KJ * 18.6,
1007 : 1. / (ANG_TO_NM * 3.5),
1008 : 0.217,
1009 : }
1010 : },
1011 : { "CC", {
1012 : ANG3_TO_NM3 * 16.539,
1013 : KCAL_TO_KJ * 0.000,
1014 : KCAL_TO_KJ * 0.000,
1015 : KCAL_TO_KJ * 0.000,
1016 : KCAL_TO_KJ * 0.0,
1017 : 1. / (ANG_TO_NM * 3.5),
1018 : 0.20,
1019 : }
1020 : },
1021 : { "CAI", {
1022 : ANG3_TO_NM3 * 18.249,
1023 : KCAL_TO_KJ * 0.057,
1024 : KCAL_TO_KJ * 0.057,
1025 : KCAL_TO_KJ * -0.973,
1026 : KCAL_TO_KJ * 6.9,
1027 : 1. / (ANG_TO_NM * 3.5),
1028 : 0.199,
1029 : }
1030 : },
1031 : { "CA", {
1032 : ANG3_TO_NM3 * 18.249,
1033 : KCAL_TO_KJ * 0.057,
1034 : KCAL_TO_KJ * 0.057,
1035 : KCAL_TO_KJ * -0.973,
1036 : KCAL_TO_KJ * 6.9,
1037 : 1. / (ANG_TO_NM * 3.5),
1038 : 0.199,
1039 : }
1040 : },
1041 : { "N", {
1042 : ANG3_TO_NM3 * 0.000,
1043 : KCAL_TO_KJ * -1.000,
1044 : KCAL_TO_KJ * -1.000,
1045 : KCAL_TO_KJ * -1.250,
1046 : KCAL_TO_KJ * 8.8,
1047 : 1. / (ANG_TO_NM * 3.5),
1048 : 0.185,
1049 : }
1050 : },
1051 : { "NR1", {
1052 : ANG3_TO_NM3 * 15.273,
1053 : KCAL_TO_KJ * -5.950,
1054 : KCAL_TO_KJ * -5.950,
1055 : KCAL_TO_KJ * -9.059,
1056 : KCAL_TO_KJ * -8.8,
1057 : 1. / (ANG_TO_NM * 3.5),
1058 : 0.185,
1059 : }
1060 : },
1061 : { "NR2", {
1062 : ANG3_TO_NM3 * 15.111,
1063 : KCAL_TO_KJ * -3.820,
1064 : KCAL_TO_KJ * -3.820,
1065 : KCAL_TO_KJ * -4.654,
1066 : KCAL_TO_KJ * -8.8,
1067 : 1. / (ANG_TO_NM * 3.5),
1068 : 0.185,
1069 : }
1070 : },
1071 : { "NR3", {
1072 : ANG3_TO_NM3 * 15.071,
1073 : KCAL_TO_KJ * -5.950,
1074 : KCAL_TO_KJ * -5.950,
1075 : KCAL_TO_KJ * -9.059,
1076 : KCAL_TO_KJ * -8.8,
1077 : 1. / (ANG_TO_NM * 3.5),
1078 : 0.185,
1079 : }
1080 : },
1081 : { "NH1", {
1082 : ANG3_TO_NM3 * 10.197,
1083 : KCAL_TO_KJ * -5.950,
1084 : KCAL_TO_KJ * -5.950,
1085 : KCAL_TO_KJ * -9.059,
1086 : KCAL_TO_KJ * -8.8,
1087 : 1. / (ANG_TO_NM * 3.5),
1088 : 0.185,
1089 : }
1090 : },
1091 : { "NH2", {
1092 : ANG3_TO_NM3 * 18.182,
1093 : KCAL_TO_KJ * -5.950,
1094 : KCAL_TO_KJ * -5.950,
1095 : KCAL_TO_KJ * -9.059,
1096 : KCAL_TO_KJ * -8.8,
1097 : 1. / (ANG_TO_NM * 3.5),
1098 : 0.185,
1099 : }
1100 : },
1101 : { "NH3", {
1102 : ANG3_TO_NM3 * 18.817,
1103 : KCAL_TO_KJ * -20.000,
1104 : KCAL_TO_KJ * -20.000,
1105 : KCAL_TO_KJ * -25.000,
1106 : KCAL_TO_KJ * -18.0,
1107 : 1. / (ANG_TO_NM * 6.0),
1108 : 0.185,
1109 : }
1110 : },
1111 : { "NC2", {
1112 : ANG3_TO_NM3 * 18.215,
1113 : KCAL_TO_KJ * -10.000,
1114 : KCAL_TO_KJ * -10.000,
1115 : KCAL_TO_KJ * -12.000,
1116 : KCAL_TO_KJ * -7.0,
1117 : 1. / (ANG_TO_NM * 6.0),
1118 : 0.185,
1119 : }
1120 : },
1121 : { "NY", {
1122 : ANG3_TO_NM3 * 12.001,
1123 : KCAL_TO_KJ * -5.950,
1124 : KCAL_TO_KJ * -5.950,
1125 : KCAL_TO_KJ * -9.059,
1126 : KCAL_TO_KJ * -8.8,
1127 : 1. / (ANG_TO_NM * 3.5),
1128 : 0.185,
1129 : }
1130 : },
1131 : { "NP", {
1132 : ANG3_TO_NM3 * 4.993,
1133 : KCAL_TO_KJ * -20.000,
1134 : KCAL_TO_KJ * -20.000,
1135 : KCAL_TO_KJ * -25.000,
1136 : KCAL_TO_KJ * -18.0,
1137 : 1. / (ANG_TO_NM * 6.0),
1138 : 0.185,
1139 : }
1140 : },
1141 : { "O", {
1142 : ANG3_TO_NM3 * 11.772,
1143 : KCAL_TO_KJ * -5.330,
1144 : KCAL_TO_KJ * -5.330,
1145 : KCAL_TO_KJ * -5.787,
1146 : KCAL_TO_KJ * -8.8,
1147 : 1. / (ANG_TO_NM * 3.5),
1148 : 0.170,
1149 : }
1150 : },
1151 : { "OB", {
1152 : ANG3_TO_NM3 * 11.694,
1153 : KCAL_TO_KJ * -5.330,
1154 : KCAL_TO_KJ * -5.330,
1155 : KCAL_TO_KJ * -5.787,
1156 : KCAL_TO_KJ * -8.8,
1157 : 1. / (ANG_TO_NM * 3.5),
1158 : 0.170,
1159 : }
1160 : },
1161 : { "OC", {
1162 : ANG3_TO_NM3 * 12.003,
1163 : KCAL_TO_KJ * -10.000,
1164 : KCAL_TO_KJ * -10.000,
1165 : KCAL_TO_KJ * -12.000,
1166 : KCAL_TO_KJ * -9.4,
1167 : 1. / (ANG_TO_NM * 6.0),
1168 : 0.170,
1169 : }
1170 : },
1171 : { "OH1", {
1172 : ANG3_TO_NM3 * 15.528,
1173 : KCAL_TO_KJ * -5.920,
1174 : KCAL_TO_KJ * -5.920,
1175 : KCAL_TO_KJ * -9.264,
1176 : KCAL_TO_KJ * -11.2,
1177 : 1. / (ANG_TO_NM * 3.5),
1178 : 0.177,
1179 : }
1180 : },
1181 : { "OS", {
1182 : ANG3_TO_NM3 * 6.774,
1183 : KCAL_TO_KJ * -2.900,
1184 : KCAL_TO_KJ * -2.900,
1185 : KCAL_TO_KJ * -3.150,
1186 : KCAL_TO_KJ * -4.8,
1187 : 1. / (ANG_TO_NM * 3.5),
1188 : 0.177,
1189 : }
1190 : },
1191 : { "S", {
1192 : ANG3_TO_NM3 * 20.703,
1193 : KCAL_TO_KJ * -3.240,
1194 : KCAL_TO_KJ * -3.240,
1195 : KCAL_TO_KJ * -4.475,
1196 : KCAL_TO_KJ * -39.9,
1197 : 1. / (ANG_TO_NM * 3.5),
1198 : 0.20,
1199 : }
1200 : },
1201 : { "SM", {
1202 : ANG3_TO_NM3 * 21.306,
1203 : KCAL_TO_KJ * -3.240,
1204 : KCAL_TO_KJ * -3.240,
1205 : KCAL_TO_KJ * -4.475,
1206 : KCAL_TO_KJ * -39.9,
1207 : 1. / (ANG_TO_NM * 3.5),
1208 : 0.197,
1209 : }
1210 : }
1211 66 : };
1212 2 : return valuemap;
1213 : }
1214 : }
1215 5517 : }
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