Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2021, Andrea Arsiccio
3 :
4 : This software is provided 'as-is', without any express or implied
5 : warranty. In no event will the authors be held liable for any damages
6 : arising from the use of this software.
7 :
8 : Permission is granted to anyone to use this software for any purpose,
9 : including commercial applications, and to alter it and redistribute it
10 : freely, subject to the following restrictions:
11 :
12 : 1. The origin of this software must not be misrepresented; you must not
13 : claim that you wrote the original software. If you use this software
14 : in a product, an acknowledgment in the product documentation would be
15 : appreciated but is not required.
16 : 2. Altered source versions must be plainly marked as such, and must not be
17 : misrepresented as being the original software.
18 : 3. This notice may not be removed or altered from any source distribution.
19 : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
20 :
21 : #include "Sasa.h"
22 : #include "ActionRegister.h"
23 : #include "core/PlumedMain.h"
24 : #include "core/GenericMolInfo.h"
25 : #include "core/ActionSet.h"
26 : #include <cstdio>
27 : #include <iostream>
28 : #include <string>
29 : #include <cmath>
30 : #include <sstream>
31 : #include <algorithm>
32 : #include <iterator>
33 : #include <fstream>
34 :
35 :
36 : using namespace std;
37 :
38 : namespace PLMD {
39 : namespace sasa {
40 :
41 : //+PLUMEDOC SASAMOD_COLVAR SASA_HASEL
42 : /*
43 : Calculates the solvent accessible surface area (SASA) of a protein molecule, or other properties related to it. The atoms for which the SASA is desired should be indicated with the keyword ATOMS, and a pdb file of the protein must be provided in input with the MOLINFO keyword. The algorithm described in \cite Hasel1988 is used for the calculation. The radius of the solvent is assumed to be 0.14 nm, which is the radius of water molecules. Using the keyword NL_STRIDE it is also possible to specify the frequency with which the neighbor list for the calculation of SASA is updated (the default is every 10 steps).
44 :
45 : Different properties can be calculated and selected using the TYPE keyword:
46 :
47 : 1) the total SASA (TOTAL);
48 :
49 : 2) the free energy of transfer for the protein according to the transfer model (TRANSFER). This keyword can be used, for instance, to compute the transfer of a protein to different temperatures, as detailed in \cite Arsiccio-T-SASA-2021, or to different pressures, as detailed in \cite Arsiccio-P-SASA-2021, or to different osmolyte solutions, as detailed in \cite Arsiccio-C-SASA-2022.
50 :
51 :
52 : When the TRANSFER keyword is used, a file with the free energy of transfer values for the sidechains and backbone atoms should be provided (using the keyword DELTAGFILE). Such file should have the following format:
53 :
54 : \verbatim
55 :
56 : ----------------Sample DeltaG.dat file---------------------
57 : ALA 0.711019999999962
58 : ARG -2.24832799999996
59 : ASN -2.74838799999999
60 : ASP -2.5626376
61 : CYS 3.89864000000006
62 : GLN -1.76192
63 : GLU -2.38664400000002
64 : GLY 0
65 : HIS -3.58152799999999
66 : ILE 2.42634399999986
67 : LEU 1.77233599999988
68 : LYS -1.92576400000002
69 : MET -0.262827999999956
70 : PHE 1.62028800000007
71 : PRO -2.15598800000001
72 : SER -1.60934800000004
73 : THR -0.591559999999987
74 : TRP 1.22936000000027
75 : TYR 0.775547999999958
76 : VAL 2.12779200000011
77 : BACKBONE 1.00066920000002
78 : -----------------------------------------------------------
79 : \endverbatim
80 :
81 : where the second column is the free energy of transfer for each sidechain/backbone, in kJ/mol.
82 :
83 : A Python script for the computation of free energy of transfer values to describe the effect of osmolyte concentration, temperature and pressure (according to \cite Arsiccio-C-SASA-2022, \cite Arsiccio-T-SASA-2021 and \cite Arsiccio-P-SASA-2021) is freely available at https://github.com/andrea-arsiccio/DeltaG-calculation. The script automatically outputs a DeltaG.dat file compatible with this SASA module.
84 :
85 :
86 : If the DELTAGFILE is not provided, the program computes the free energy of transfer values as if they had to take into account the effect of temperature according to approaches 2 or 3 in the paper \cite Arsiccio-T-SASA-2021. Please read and cite this paper if using the transfer model for computing the effect of temperature in implicit solvent simulations. For this purpose, the keyword APPROACH should be added, and set to either 2 or 3.
87 :
88 : The SASA usually makes sense when atoms used for the calculation are all part of the same molecule. When running with periodic boundary conditions, the atoms should be in the proper periodic image. This is done automatically since PLUMED 2.2, by considering the ordered list of atoms and rebuilding the broken entities using a procedure that is equivalent to that done in \ref WHOLEMOLECULES. Notice that rebuilding is local to this action. This is different from \ref WHOLEMOLECULES which actually modifies the coordinates stored in PLUMED.
89 :
90 : In case you want to recover the old behavior you should use the NOPBC flag.
91 : In that case you need to take care that atoms are in the correct periodic image.
92 :
93 : The SASA may also be computed using the SASA_LCPO collective variable, which makes use of the LCPO algorithm \cite Weiser1999. SASA_LCPO is more accurate then SASA_HASEL, but the computation is slower.
94 :
95 :
96 : \par Examples
97 :
98 : The following input tells plumed to print the total SASA for atoms 10 to 20 in a protein chain.
99 : \plumedfile
100 : SASA_HASEL TYPE=TOTAL ATOMS=10-20 NL_STRIDE=10 LABEL=sasa
101 : PRINT ARG=sasa STRIDE=1 FILE=colvar
102 : \endplumedfile
103 :
104 :
105 : The following input tells plumed to compute the transfer free energy for the protein chain containing atoms 10 to 20. Such transfer free energy is then used as a bias in the simulation (e.g., implicit solvent simulations). The free energy of transfer values are read from a file called DeltaG.dat.
106 :
107 : \plumedfile
108 : SASA_HASEL TYPE=TRANSFER ATOMS=10-20 NL_STRIDE=10 DELTAGFILE=DeltaG.dat LABEL=sasa
109 :
110 : bias: BIASVALUE ARG=sasa
111 :
112 : PRINT ARG=sasa,bias.* STRIDE=1 FILE=colvar
113 : \endplumedfile
114 :
115 : The following input tells plumed to compute the transfer free energy for the protein chain containing atoms 10 to 20. Such transfer free energy is then used as a bias in the simulation (e.g., implicit solvent simulations). The free energy of transfer values are computed according to \cite Arsiccio-T-SASA-2021, and take into account the effect of temperature using approach 2 as described in the paper.
116 :
117 : \plumedfile
118 : SASA_HASEL TYPE=TRANSFER ATOMS=10-20 NL_STRIDE=10 APPROACH=2 LABEL=sasa
119 :
120 : bias: BIASVALUE ARG=sasa
121 :
122 : PRINT ARG=sasa,bias.* STRIDE=1 FILE=colvar
123 : \endplumedfile
124 :
125 : */
126 : //+ENDPLUMEDOC
127 :
128 : class SASA_HASEL : public Colvar {
129 : private:
130 : enum CV_TYPE {TOTAL, TRANSFER};
131 : int sasa_type;
132 : bool nopbc;
133 : double rs;
134 : string DeltaGValues;
135 : int approach;
136 : unsigned stride;
137 : unsigned nl_update;
138 : int firstStepFlag;
139 : double Ti;
140 : // cppcheck-suppress duplInheritedMember
141 : std::vector<AtomNumber> atoms;
142 : vector < vector < std::string > > AtomResidueName;
143 : vector < vector < double > > SASAparam;
144 : vector < vector < std::string > > CONNECTparam;
145 : unsigned natoms;
146 : vector < vector < double > > MaxSurf;
147 : vector < vector < double > > DeltaG;
148 : vector < vector < int > > Nlist;
149 : public:
150 : static void registerKeywords(Keywords& keys);
151 : explicit SASA_HASEL(const ActionOptions&);
152 : void readPDB();
153 : map<string, vector<std::string> > setupHASELparam();
154 : void readSASAparam();
155 : void calcNlist();
156 : map<string, vector<double> > setupMaxSurfMap();
157 : void readMaxSurf();
158 : void readDeltaG();
159 : void computeDeltaG();
160 : virtual void calculate();
161 : };
162 :
163 10423 : PLUMED_REGISTER_ACTION(SASA_HASEL,"SASA_HASEL")
164 :
165 3 : void SASA_HASEL::registerKeywords(Keywords& keys) {
166 3 : Colvar::registerKeywords(keys);
167 6 : keys.add("atoms","ATOMS","the group of atoms that you are calculating the SASA for");
168 6 : keys.add("compulsory","TYPE","TOTAL","The type of calculation you want to perform. Can be TOTAL or TRANSFER");
169 6 : keys.add("compulsory", "NL_STRIDE", "The frequency with which the neighbor list for the calculation of SASA is updated.");
170 6 : keys.add("optional","DELTAGFILE","a file containing the free energy of transfer values for backbone and sidechains atoms. Necessary only if TYPE = TRANSFER. A Python script for the computation of free energy of transfer values to describe the effect of osmolyte concentration, temperature and pressure is freely available at https://github.com/andrea-arsiccio/DeltaG-calculation. The script automatically outputs a DeltaG.dat file compatible with this SASA module. If TYPE = TRANSFER and no DELTAGFILE is provided, the free energy values are those describing the effect of temperature, and are computed using the temperature value passed by the MD engine");
171 6 : keys.add("optional","APPROACH","either approach 2 or 3. Necessary only if TYPE = TRANSFER and no DELTAGFILE is provided. If TYPE = TRANSFER and no DELTAGFILE is provided, the free energy values are those describing the effect of temperature, and the program must know if approach 2 or 3 (as described in Arsiccio and Shea, Protein Cold Denaturation in Implicit Solvent Simulations: A Transfer Free Energy Approach, J. Phys. Chem. B, 2021) needs to be used to compute them");
172 3 : }
173 :
174 :
175 2 : SASA_HASEL::SASA_HASEL(const ActionOptions&ao):
176 : PLUMED_COLVAR_INIT(ao),
177 2 : nopbc(false),
178 2 : stride(10),
179 2 : nl_update(0),
180 4 : DeltaGValues("absent"),
181 2 : Ti(0),
182 2 : firstStepFlag(0)
183 : {
184 2 : rs = 0.14;
185 2 : parse("DELTAGFILE",DeltaGValues);
186 2 : parse("APPROACH", approach);
187 4 : parseAtomList("ATOMS",atoms);
188 2 : if(atoms.size()==0) error("no atoms specified");
189 : std::string Type;
190 2 : parse("TYPE",Type);
191 2 : parse("NL_STRIDE", stride);
192 2 : parseFlag("NOPBC",nopbc);
193 2 : checkRead();
194 :
195 2 : if(Type=="TOTAL") sasa_type=TOTAL;
196 1 : else if(Type=="TRANSFER") sasa_type=TRANSFER;
197 0 : else error("Unknown SASA type");
198 :
199 2 : switch(sasa_type)
200 : {
201 1 : case TOTAL: log.printf(" TOTAL SASA;"); break;
202 1 : case TRANSFER: log.printf(" TRANSFER MODEL;"); break;
203 : }
204 :
205 2 : log.printf(" atoms involved : ");
206 242 : for(unsigned i=0; i<atoms.size(); ++i) {
207 240 : if(i%25==0) log<<"\n";
208 240 : log.printf("%d ",atoms[i].serial());
209 : }
210 2 : log.printf("\n");
211 :
212 2 : if(nopbc) {
213 0 : log<<" PBC will be ignored\n";
214 : } else {
215 2 : log<<" broken molecules will be rebuilt assuming atoms are in the proper order\n";
216 : }
217 :
218 :
219 2 : addValueWithDerivatives(); setNotPeriodic();
220 2 : requestAtoms(atoms);
221 :
222 2 : natoms = getNumberOfAtoms();
223 2 : AtomResidueName.resize(2);
224 2 : SASAparam.resize(natoms);
225 2 : CONNECTparam.resize(natoms);
226 2 : MaxSurf.resize(natoms);
227 2 : DeltaG.resize(natoms+1);
228 2 : Nlist.resize(natoms);
229 :
230 :
231 2 : }
232 :
233 :
234 : //splits strings into tokens. Used to read into SASA parameters file and into reference pdb file
235 : template <class Container>
236 42 : void split(const std::string& str, Container& cont)
237 : {
238 42 : std::istringstream iss(str);
239 84 : std::copy(std::istream_iterator<std::string>(iss),
240 42 : std::istream_iterator<std::string>(),
241 : std::back_inserter(cont));
242 42 : }
243 :
244 :
245 : //reads input PDB file provided with MOLINFO, and assigns atom and residue names to each atom involved in the CV
246 :
247 2 : void SASA_HASEL::readPDB() {
248 2 : auto* moldat = plumed.getActionSet().selectLatest<GenericMolInfo*>(this);
249 2 : if( ! moldat ) error("Unable to find MOLINFO in input");
250 2 : AtomResidueName[0].clear();
251 2 : AtomResidueName[1].clear();
252 :
253 242 : for(unsigned i=0; i<natoms; i++) {
254 240 : string Aname = moldat->getAtomName(atoms[i]);
255 240 : string Rname = moldat->getResidueName(atoms[i]);
256 240 : AtomResidueName[0].push_back (Aname);
257 240 : AtomResidueName[1].push_back (Rname);
258 : }
259 :
260 2 : }
261 :
262 :
263 : //Hasel et al. parameters database
264 2 : map<string, vector<std::string> > SASA_HASEL::setupHASELparam() {
265 : map<string, vector<std::string> > haselmap;
266 16 : haselmap["ALA_N"] = { "1.55", "1.028", "H", "CA", "Z", "Z", };
267 16 : haselmap["ALA_CA"] = { "1.7", "2.149", "N", "C", "CB", "Z", };
268 16 : haselmap["ALA_C"] = { "1.72", "1.554", "CA", "O", "Z", "Z", };
269 16 : haselmap["ALA_O"] = { "1.5", "0.926", "C", "Z", "Z", "Z", };
270 16 : haselmap["ALA_H"] = { "1.1", "1.128", "N", "Z", "Z", "Z", };
271 16 : haselmap["ALA_CB"] = { "2.0", "0.88", "CA", "Z", "Z", "Z", };
272 16 : haselmap["ASP_N"] = { "1.55", "1.028", "H", "CA", "Z", "Z", };
273 16 : haselmap["ASP_CA"] = { "1.7", "2.149", "N", "C", "CB", "Z", };
274 16 : haselmap["ASP_C"] = { "1.72", "1.554", "CA", "O", "Z", "Z", };
275 16 : haselmap["ASP_O"] = { "1.5", "0.926", "C", "Z", "Z", "Z", };
276 16 : haselmap["ASP_H"] = { "1.1", "1.128", "N", "Z", "Z", "Z", };
277 16 : haselmap["ASP_CB"] = { "1.9", "1.045", "CA", "CG", "Z", "Z", };
278 16 : haselmap["ASP_CG"] = { "1.72", "1.554", "CB", "OD1", "OD2", "Z", };
279 16 : haselmap["ASP_OD1"] = { "1.5", "0.926", "CG", "Z", "Z", "Z", };
280 16 : haselmap["ASP_OD2"] = { "1.7", "0.922", "CG", "Z", "Z", "Z", };
281 16 : haselmap["ASN_N"] = { "1.55", "1.028", "H", "CA", "Z", "Z", };
282 16 : haselmap["ASN_CA"] = { "1.7", "2.149", "N", "C", "CB", "Z", };
283 16 : haselmap["ASN_C"] = { "1.72", "1.554", "CA", "O", "Z", "Z", };
284 16 : haselmap["ASN_O"] = { "1.5", "0.926", "C", "Z", "Z", "Z", };
285 16 : haselmap["ASN_H"] = { "1.1", "1.128", "N", "Z", "Z", "Z", };
286 16 : haselmap["ASN_CB"] = { "1.9", "1.045", "CA", "CG", "Z", "Z", };
287 16 : haselmap["ASN_CG"] = { "1.7", "2.149", "CB", "OD1", "ND2", "Z", };
288 16 : haselmap["ASN_OD1"] = { "1.5", "0.926", "CG", "Z", "Z", "Z", };
289 16 : haselmap["ASN_ND2"] = { "1.6", "1.215", "CG", "1HD2", "1HD2", "Z", };
290 16 : haselmap["ASN_1HD2"] = { "1.1", "1.128", "ND2", "Z", "Z", "Z", };
291 16 : haselmap["ASN_2HD2"] = { "1.1", "1.128", "ND2", "Z", "Z", "Z", };
292 16 : haselmap["ARG_N"] = { "1.55", "1.028", "H", "CA", "Z", "Z", };
293 16 : haselmap["ARG_CA"] = { "1.7", "2.149", "N", "C", "CB", "Z", };
294 16 : haselmap["ARG_C"] = { "1.72", "1.554", "CA", "O", "Z", "Z", };
295 16 : haselmap["ARG_O"] = { "1.5", "0.926", "C", "Z", "Z", "Z", };
296 16 : haselmap["ARG_H"] = { "1.1", "1.128", "N", "Z", "Z", "Z", };
297 16 : haselmap["ARG_CB"] = { "1.9", "1.045", "CA", "CG", "Z", "Z", };
298 16 : haselmap["ARG_CG"] = { "1.9", "1.045", "CB", "CD", "Z", "Z", };
299 16 : haselmap["ARG_CD"] = { "1.9", "1.045", "CG", "NE", "Z", "Z", };
300 16 : haselmap["ARG_NE"] = { "1.55", "1.028", "CD", "HE", "CZ", "Z", };
301 16 : haselmap["ARG_NH1"] = { "1.55", "1.028", "CZ", "1HH1", "2HH1", "Z", };
302 16 : haselmap["ARG_NH2"] = { "1.55", "1.028", "CZ", "1HH2", "2HH2", "Z", };
303 16 : haselmap["ARG_CZ"] = { "1.72", "1.554", "NE", "NH1", "NH2", "Z", };
304 16 : haselmap["ARG_HE"] = { "1.1", "1.128", "NE", "Z", "Z", "Z", };
305 16 : haselmap["ARG_1HH2"] = { "1.1", "1.128", "NH2", "Z", "Z", "Z", };
306 16 : haselmap["ARG_2HH2"] = { "1.1", "1.128", "NH2", "Z", "Z", "Z", };
307 16 : haselmap["ARG_2HH1"] = { "1.1", "1.128", "NH1", "Z", "Z", "Z", };
308 16 : haselmap["ARG_1HH1"] = { "1.1", "1.128", "NH1", "Z", "Z", "Z", };
309 16 : haselmap["CYS_N"] = { "1.55", "1.028", "H", "CA", "Z", "Z", };
310 16 : haselmap["CYS_CA"] = { "1.7", "2.149", "N", "C", "CB", "Z", };
311 16 : haselmap["CYS_C"] = { "1.72", "1.554", "CA", "O", "Z", "Z", };
312 16 : haselmap["CYS_O"] = { "1.5", "0.926", "C", "Z", "Z", "Z", };
313 16 : haselmap["CYS_H"] = { "1.1", "1.128", "N", "Z", "Z", "Z", };
314 16 : haselmap["CYS_CB"] = { "1.9", "1.045", "CA", "SG", "Z", "Z", };
315 16 : haselmap["CYS_SG"] = { "1.8", "1.121", "CB", "HG", "Z", "Z", };
316 16 : haselmap["CYS_HG"] = { "1.2", "0.928", "SG", "Z", "Z", "Z", };
317 16 : haselmap["GLU_N"] = { "1.55", "1.028", "H", "CA", "Z", "Z", };
318 16 : haselmap["GLU_CA"] = { "1.7", "2.149", "N", "C", "CB", "Z", };
319 16 : haselmap["GLU_C"] = { "1.72", "1.554", "CA", "O", "Z", "Z", };
320 16 : haselmap["GLU_O"] = { "1.5", "0.926", "C", "Z", "Z", "Z", };
321 16 : haselmap["GLU_H"] = { "1.1", "1.128", "N", "Z", "Z", "Z", };
322 16 : haselmap["GLU_CB"] = { "1.9", "1.045", "CA", "CG", "Z", "Z", };
323 16 : haselmap["GLU_CG"] = { "1.9", "1.045", "CB", "CD", "Z", "Z", };
324 16 : haselmap["GLU_CD"] = { "1.72", "1.554", "CG", "OE1", "OE2", "Z", };
325 16 : haselmap["GLU_OE1"] = { "1.5", "0.926", "CD", "Z", "Z", "Z", };
326 16 : haselmap["GLU_OE2"] = { "1.7", "0.922", "CD", "Z", "Z", "Z", };
327 16 : haselmap["GLN_N"] = { "1.55", "1.028", "H", "CA", "Z", "Z", };
328 16 : haselmap["GLN_CA"] = { "1.7", "2.149", "N", "C", "CB", "Z", };
329 16 : haselmap["GLN_C"] = { "1.72", "1.554", "CA", "O", "Z", "Z", };
330 16 : haselmap["GLN_O"] = { "1.5", "0.926", "C", "Z", "Z", "Z", };
331 16 : haselmap["GLN_H"] = { "1.1", "1.128", "N", "Z", "Z", "Z", };
332 16 : haselmap["GLN_CB"] = { "1.9", "1.045", "CA", "CG", "Z", "Z", };
333 16 : haselmap["GLN_CG"] = { "1.9", "1.045", "CB", "CD", "Z", "Z", };
334 16 : haselmap["GLN_CD"] = { "1.72", "1.554", "CG", "OE1", "NE2", "Z", };
335 16 : haselmap["GLN_OE1"] = { "1.5", "0.926", "CD", "Z", "Z", "Z", };
336 16 : haselmap["GLN_NE2"] = { "1.6", "1.215", "CD", "2HE2", "1HE2", "Z", };
337 16 : haselmap["GLN_2HE2"] = { "1.1", "1.128", "NE2", "Z", "Z", "Z", };
338 16 : haselmap["GLN_1HE2"] = { "1.1", "1.128", "NE2", "Z", "Z", "Z", };
339 16 : haselmap["GLY_N"] = { "1.55", "1.028", "H", "CA", "Z", "Z", };
340 16 : haselmap["GLY_CA"] = { "1.7", "2.149", "N", "C", "Z", "Z", };
341 16 : haselmap["GLY_C"] = { "1.72", "1.554", "CA", "O", "Z", "Z", };
342 16 : haselmap["GLY_O"] = { "1.5", "0.926", "C", "Z", "Z", "Z", };
343 16 : haselmap["GLY_H"] = { "1.1", "1.128", "N", "Z", "Z", "Z", };
344 16 : haselmap["HIS_N"] = { "1.55", "1.028", "H", "CA", "Z", "Z", };
345 16 : haselmap["HIS_CA"] = { "1.7", "2.149", "N", "C", "CB", "Z", };
346 16 : haselmap["HIS_C"] = { "1.72", "1.554", "CA", "O", "Z", "Z", };
347 16 : haselmap["HIS_O"] = { "1.5", "0.926", "C", "Z", "Z", "Z", };
348 16 : haselmap["HIS_H"] = { "1.1", "1.128", "N", "Z", "Z", "Z", };
349 16 : haselmap["HIS_CB"] = { "1.9", "1.045", "CA", "CG", "Z", "Z", };
350 16 : haselmap["HIS_CG"] = { "1.72", "1.554", "CB", "CD2", "ND1", "Z", };
351 16 : haselmap["HIS_ND1"] = { "1.55", "1.028", "CG", "CE1", "Z", "Z", };
352 16 : haselmap["HIS_CE1"] = { "1.8", "1.073", "ND1", "NE2", "Z", "Z", };
353 16 : haselmap["HIS_NE2"] = { "1.55", "1.413", "CE1", "2HE", "CD2", "Z", };
354 16 : haselmap["HIS_CD2"] = { "1.8", "1.073", "NE2", "CG", "Z", "Z", };
355 16 : haselmap["HIS_2HE"] = { "1.1", "1.128", "NE2", "Z", "Z", "Z", };
356 16 : haselmap["ILE_N"] = { "1.55", "1.028", "H", "CA", "Z", "Z", };
357 16 : haselmap["ILE_CA"] = { "1.7", "2.149", "N", "C", "CB", "Z", };
358 16 : haselmap["ILE_C"] = { "1.72", "1.554", "CA", "O", "Z", "Z", };
359 16 : haselmap["ILE_O"] = { "1.5", "0.926", "C", "Z", "Z", "Z", };
360 16 : haselmap["ILE_H"] = { "1.1", "1.128", "N", "Z", "Z", "Z", };
361 16 : haselmap["ILE_CB"] = { "1.8", "1.276", "CA", "CG2", "CG1", "Z", };
362 16 : haselmap["ILE_CG2"] = { "2.0", "0.88", "CB", "Z", "Z", "Z", };
363 16 : haselmap["ILE_CG1"] = { "1.9", "1.045", "CB", "CD1", "Z", "Z", };
364 16 : haselmap["ILE_CD1"] = { "2.0", "0.88", "CG1", "Z", "Z", "Z", };
365 16 : haselmap["LEU_N"] = { "1.55", "1.028", "H", "CA", "Z", "Z", };
366 16 : haselmap["LEU_CA"] = { "1.7", "2.149", "N", "C", "CB", "Z", };
367 16 : haselmap["LEU_C"] = { "1.72", "1.554", "CA", "O", "Z", "Z", };
368 16 : haselmap["LEU_O"] = { "1.5", "0.926", "C", "Z", "Z", "Z", };
369 16 : haselmap["LEU_H"] = { "1.1", "1.128", "N", "Z", "Z", "Z", };
370 16 : haselmap["LEU_CB"] = { "1.9", "1.045", "CA", "CG", "Z", "Z", };
371 16 : haselmap["LEU_CG"] = { "1.8", "1.276", "CB", "CD1", "CD2", "Z", };
372 16 : haselmap["LEU_CD1"] = { "2.0", "0.88", "CG", "Z", "Z", "Z", };
373 16 : haselmap["LEU_CD2"] = { "2.0", "0.88", "CG", "Z", "Z", "Z", };
374 16 : haselmap["LYS_N"] = { "1.55", "1.028", "H", "CA", "Z", "Z", };
375 16 : haselmap["LYS_CA"] = { "1.7", "2.149", "N", "C", "CB", "Z", };
376 16 : haselmap["LYS_C"] = { "1.72", "1.554", "CA", "O", "Z", "Z", };
377 16 : haselmap["LYS_O"] = { "1.5", "0.926", "C", "Z", "Z", "Z", };
378 16 : haselmap["LYS_H"] = { "1.1", "1.128", "N", "Z", "Z", "Z", };
379 16 : haselmap["LYS_CB"] = { "1.9", "1.045", "CA", "CG", "Z", "Z", };
380 16 : haselmap["LYS_CG"] = { "1.9", "1.045", "CB", "CD", "Z", "Z", };
381 16 : haselmap["LYS_CD"] = { "1.9", "1.045", "CG", "CE", "Z", "Z", };
382 16 : haselmap["LYS_CE"] = { "1.9", "1.045", "CD", "NZ", "Z", "Z", };
383 16 : haselmap["LYS_NZ"] = { "1.6", "1.215", "CE", "1HZ", "2HZ", "3HZ", };
384 16 : haselmap["LYS_1HZ"] = { "1.1", "1.128", "NZ", "Z", "Z", "Z", };
385 16 : haselmap["LYS_2HZ"] = { "1.1", "1.128", "NZ", "Z", "Z", "Z", };
386 16 : haselmap["LYS_3HZ"] = { "1.1", "1.128", "NZ", "Z", "Z", "Z", };
387 16 : haselmap["MET_N"] = { "1.55", "1.028", "H", "CA", "Z", "Z", };
388 16 : haselmap["MET_CA"] = { "1.7", "2.149", "N", "C", "CB", "Z", };
389 16 : haselmap["MET_C"] = { "1.72", "1.554", "CA", "O", "Z", "Z", };
390 16 : haselmap["MET_O"] = { "1.5", "0.926", "C", "Z", "Z", "Z", };
391 16 : haselmap["MET_H"] = { "1.1", "1.128", "N", "Z", "Z", "Z", };
392 16 : haselmap["MET_CB"] = { "1.9", "1.045", "CA", "CG", "Z", "Z", };
393 16 : haselmap["MET_CG"] = { "1.9", "1.045", "CB", "SD", "Z", "Z", };
394 16 : haselmap["MET_SD"] = { "1.8", "1.121", "CG", "CE", "Z", "Z", };
395 16 : haselmap["MET_CE"] = { "2.0", "0.88", "SD", "Z", "Z", "Z", };
396 16 : haselmap["PHE_N"] = { "1.55", "1.028", "H", "CA", "Z", "Z", };
397 16 : haselmap["PHE_CA"] = { "1.7", "2.149", "N", "C", "CB", "Z", };
398 16 : haselmap["PHE_C"] = { "1.72", "1.554", "CA", "O", "Z", "Z", };
399 16 : haselmap["PHE_O"] = { "1.5", "0.926", "C", "Z", "Z", "Z", };
400 16 : haselmap["PHE_H"] = { "1.1", "1.128", "N", "Z", "Z", "Z", };
401 16 : haselmap["PHE_CB"] = { "1.9", "1.045", "CA", "CG", "Z", "Z", };
402 16 : haselmap["PHE_CG"] = { "1.72", "1.554", "CB", "CD1", "CD2", "Z", };
403 16 : haselmap["PHE_CD1"] = { "1.8", "1.073", "CG", "CE1", "Z", "Z", };
404 16 : haselmap["PHE_CE1"] = { "1.8", "1.073", "CD1", "CZ", "Z", "Z", };
405 16 : haselmap["PHE_CZ"] = { "1.8", "1.073", "CE1", "CE2", "Z", "Z", };
406 16 : haselmap["PHE_CE2"] = { "1.8", "1.073", "CZ", "CD2", "Z", "Z", };
407 16 : haselmap["PHE_CD2"] = { "1.8", "1.073", "CE2", "CG", "Z", "Z", };
408 16 : haselmap["PRO_N"] = { "1.55", "1.028", "CD", "CA", "Z", "Z", };
409 16 : haselmap["PRO_CA"] = { "1.7", "2.149", "N", "C", "CB", "Z", };
410 16 : haselmap["PRO_C"] = { "1.72", "1.554", "CA", "O", "Z", "Z", };
411 16 : haselmap["PRO_O"] = { "1.5", "0.926", "C", "Z", "Z", "Z", };
412 16 : haselmap["PRO_CB"] = { "1.9", "1.045", "CA", "CG", "Z", "Z", };
413 16 : haselmap["PRO_CG"] = { "1.9", "1.045", "CB", "CD", "Z", "Z", };
414 16 : haselmap["PRO_CD"] = { "1.9", "1.045", "CG", "N", "Z", "Z", };
415 16 : haselmap["SER_N"] = { "1.55", "1.028", "H", "CA", "Z", "Z", };
416 16 : haselmap["SER_CA"] = { "1.7", "2.149", "N", "C", "CB", "Z", };
417 16 : haselmap["SER_C"] = { "1.72", "1.554", "CA", "O", "Z", "Z", };
418 16 : haselmap["SER_O"] = { "1.5", "0.926", "C", "Z", "Z", "Z", };
419 16 : haselmap["SER_H"] = { "1.1", "1.128", "N", "Z", "Z", "Z", };
420 16 : haselmap["SER_CB"] = { "1.9", "1.045", "CA", "OG", "Z", "Z", };
421 16 : haselmap["SER_OG"] = { "1.52", "1.08", "CB", "HG", "Z", "Z", };
422 16 : haselmap["SER_HG"] = { "1.0", "0.944", "OG", "Z", "Z", "Z", };
423 16 : haselmap["THR_N"] = { "1.55", "1.028", "H", "CA", "Z", "Z", };
424 16 : haselmap["THR_CA"] = { "1.7", "2.149", "N", "C", "CB", "Z", };
425 16 : haselmap["THR_C"] = { "1.72", "1.554", "CA", "O", "Z", "Z", };
426 16 : haselmap["THR_O"] = { "1.5", "0.926", "C", "Z", "Z", "Z", };
427 16 : haselmap["THR_H"] = { "1.1", "1.128", "N", "Z", "Z", "Z", };
428 16 : haselmap["THR_CB"] = { "1.8", "1.276", "CA", "CG2", "OG1", "Z", };
429 16 : haselmap["THR_CG2"] = { "2.0", "0.88", "CB", "Z", "Z", "Z", };
430 16 : haselmap["THR_OG1"] = { "1.52", "1.08", "1HG", "CB", "Z", "Z", };
431 16 : haselmap["THR_1HG"] = { "1.0", "0.944", "OG1", "Z", "Z", "Z", };
432 16 : haselmap["TRP_N"] = { "1.55", "1.028", "H", "CA", "Z", "Z", };
433 16 : haselmap["TRP_CA"] = { "1.7", "2.149", "N", "C", "CB", "Z", };
434 16 : haselmap["TRP_C"] = { "1.72", "1.554", "CA", "O", "Z", "Z", };
435 16 : haselmap["TRP_O"] = { "1.5", "0.926", "C", "Z", "Z", "Z", };
436 16 : haselmap["TRP_H"] = { "1.1", "1.128", "N", "Z", "Z", "Z", };
437 16 : haselmap["TRP_CB"] = { "1.9", "1.045", "CA", "CG", "Z", "Z", };
438 16 : haselmap["TRP_CG"] = { "1.72", "1.554", "CB", "CD2", "CD1", "Z", };
439 16 : haselmap["TRP_CD1"] = { "1.8", "1.073", "CG", "NE1", "Z", "Z", };
440 16 : haselmap["TRP_NE1"] = { "1.55", "1.413", "CD1", "CE2", "1HE", "Z", };
441 16 : haselmap["TRP_CE2"] = { "1.72", "1.554", "NE1", "CD2", "CZ2", "Z", };
442 16 : haselmap["TRP_CZ2"] = { "1.8", "1.073", "CE2", "CH2", "Z", "Z", };
443 16 : haselmap["TRP_CH2"] = { "1.8", "1.073", "CZ2", "CZ3", "Z", "Z", };
444 16 : haselmap["TRP_CZ3"] = { "1.8", "1.073", "CH2", "CE3", "Z", "Z", };
445 16 : haselmap["TRP_CE3"] = { "1.8", "1.073", "CZ3", "CD2", "Z", "Z", };
446 16 : haselmap["TRP_CD2"] = { "1.72", "1.554", "CE3", "CE2", "CG", "Z", };
447 16 : haselmap["TRP_1HE"] = { "1.1", "1.128", "NE1", "Z", "Z", "Z", };
448 16 : haselmap["TYR_N"] = { "1.55", "1.028", "H", "CA", "Z", "Z", };
449 16 : haselmap["TYR_CA"] = { "1.7", "2.149", "N", "C", "CB", "Z", };
450 16 : haselmap["TYR_C"] = { "1.72", "1.554", "CA", "O", "Z", "Z", };
451 16 : haselmap["TYR_O"] = { "1.5", "0.926", "C", "Z", "Z", "Z", };
452 16 : haselmap["TYR_H"] = { "1.1", "1.128", "N", "Z", "Z", "Z", };
453 16 : haselmap["TYR_CB"] = { "1.9", "1.045", "CA", "CG", "Z", "Z", };
454 16 : haselmap["TYR_CG"] = { "1.72", "1.554", "CB", "CD1", "CD2", "Z", };
455 16 : haselmap["TYR_CD1"] = { "1.8", "1.073", "CG", "CE1", "Z", "Z", };
456 16 : haselmap["TYR_CE1"] = { "1.8", "1.073", "CD1", "CZ", "Z", "Z", };
457 16 : haselmap["TYR_CZ"] = { "1.72", "1.554", "CE1", "OH", "CE2", "Z", };
458 16 : haselmap["TYR_OH"] = { "1.52", "1.08", "CZ", "HH", "Z", "Z", };
459 16 : haselmap["TYR_HH"] = { "1.0", "0.944", "OH", "Z", "Z", "Z", };
460 16 : haselmap["TYR_CE2"] = { "1.8", "1.073", "CZ", "CD2", "Z", "Z", };
461 16 : haselmap["TYR_CD2"] = { "1.8", "1.073", "CE2", "CG", "Z", "Z", };
462 16 : haselmap["VAL_N"] = { "1.55", "1.028", "H", "CA", "Z", "Z", };
463 16 : haselmap["VAL_CA"] = { "1.7", "2.149", "N", "C", "CB", "Z", };
464 16 : haselmap["VAL_C"] = { "1.72", "1.554", "CA", "O", "Z", "Z", };
465 16 : haselmap["VAL_O"] = { "1.5", "0.926", "C", "Z", "Z", "Z", };
466 16 : haselmap["VAL_H"] = { "1.1", "1.128", "N", "Z", "Z", "Z", };
467 16 : haselmap["VAL_CB"] = { "1.8", "1.276", "CA", "CG1", "CG2", "Z", };
468 16 : haselmap["VAL_CG1"] = { "2.0", "0.88", "CB", "Z", "Z", "Z", };
469 16 : haselmap["VAL_CG2"] = { "2.0", "0.88", "CB", "Z", "Z", "Z", };
470 2 : return haselmap;
471 : }
472 :
473 : //assigns SASA parameters to each atom reading from HASEL parameter database
474 2 : void SASA_HASEL::readSASAparam() {
475 :
476 242 : for(unsigned i=0; i<natoms; i++) {
477 240 : SASAparam[i].clear();
478 240 : CONNECTparam[i].clear();
479 : }
480 :
481 : map<string, vector<std::string> > haselmap;
482 4 : haselmap = setupHASELparam();
483 : vector<std::string> HASELparamVector;
484 : string identifier;
485 :
486 :
487 242 : for(unsigned i=0; i<natoms; i++) {
488 480 : identifier = AtomResidueName[1][i]+"_"+AtomResidueName[0][i];
489 240 : if (haselmap.find(identifier)!=haselmap.end()) {
490 144 : HASELparamVector = haselmap.at(identifier);
491 144 : SASAparam[i].push_back (std::atof(HASELparamVector[0].c_str())+rs*10);
492 144 : SASAparam[i].push_back (std::atof(HASELparamVector[1].c_str()));
493 288 : CONNECTparam[i].push_back (HASELparamVector[2].c_str());
494 288 : CONNECTparam[i].push_back (HASELparamVector[3].c_str());
495 288 : CONNECTparam[i].push_back (HASELparamVector[4].c_str());
496 288 : CONNECTparam[i].push_back (HASELparamVector[5].c_str());
497 : }
498 : }
499 :
500 :
501 242 : for(unsigned i=0; i<natoms; i++) {
502 240 : if (SASAparam[i].size()==0 ) {
503 96 : if ((AtomResidueName[0][i][0]=='O') || (AtomResidueName[0][i][0]=='N') || (AtomResidueName[0][i][0]=='C') || (AtomResidueName[0][i][0]=='S')) {
504 0 : cout << "Could not find SASA paramaters for atom " << AtomResidueName[0][i] << " of residue " << AtomResidueName[1][i] << endl;
505 0 : error ("missing SASA parameters\n");
506 : }
507 : }
508 : }
509 :
510 :
511 4 : }
512 :
513 :
514 :
515 : //Max Surf values, used only if TYPE=TRANSFER
516 1 : map<string, vector<double> > SASA_HASEL::setupMaxSurfMap() {
517 : // Max Surface Area for backbone and sidechain, in nm2
518 : map<string, vector<double> > valuemap;
519 1 : valuemap ["ALA"]= {0.56425,0.584851,};
520 1 : valuemap ["ARG"]= {0.498656,1.808093,};
521 1 : valuemap ["ASN"]= {0.473409,0.818394,};
522 1 : valuemap ["ASP"]= {0.477057,0.977303,};
523 1 : valuemap ["CYS"]= {0.507512,0.791483,};
524 1 : valuemap ["GLN"]= {0.485859,1.281534,};
525 1 : valuemap ["GLU"]= {0.495054,1.464718,};
526 1 : valuemap ["GLY"]= {0.658632,0,};
527 1 : valuemap ["HIS"]= {0.48194,1.118851,};
528 1 : valuemap ["ILE"]= {0.461283,1.450569,};
529 1 : valuemap ["LEU"]= {0.476315,1.498843,};
530 1 : valuemap ["LYS"]= {0.493533,1.619731,};
531 1 : valuemap ["MET"]= {0.507019,1.631904,};
532 1 : valuemap ["PHE"]= {0.457462, 1.275125,};
533 1 : valuemap ["PRO"]= {0.315865,0.859456,};
534 1 : valuemap ["SER"]= {0.48636,0.627233,};
535 1 : valuemap ["THR"]= {0.45064,0.91088,};
536 1 : valuemap ["TRP"]= {0.45762,1.366369,};
537 1 : valuemap ["TYR"]= {0.461826,1.425822,};
538 1 : valuemap ["VAL"]= {0.477054,1.149101,};
539 1 : return valuemap;
540 : }
541 :
542 :
543 :
544 : //reads maximum surface values per residue type and assigns values to each atom, only used if sasa_type = TRANSFER
545 :
546 1 : void SASA_HASEL::readMaxSurf() {
547 : map<string, vector<double> > valuemap;
548 2 : valuemap = setupMaxSurfMap();
549 : vector<double> MaxSurfVector;
550 :
551 121 : for(unsigned i=0; i<natoms; i++) {
552 120 : MaxSurf[i].clear();
553 120 : MaxSurfVector = valuemap.at(AtomResidueName[1][i]);
554 120 : MaxSurf[i].push_back (MaxSurfVector[0]*100);
555 120 : MaxSurf[i].push_back (MaxSurfVector[1]*100);
556 : }
557 1 : }
558 :
559 : //reads file with free energy values for sidechains and for the backbone, and assigns values to each atom. Only used if sasa_type = TRANSFER
560 :
561 1 : void SASA_HASEL::readDeltaG() {
562 :
563 121 : for(unsigned i=0; i<natoms; i++) {
564 120 : DeltaG[i].clear();
565 : }
566 :
567 : string DeltaGline;
568 1 : fstream DeltaGFile;
569 1 : DeltaGFile.open(DeltaGValues);
570 1 : if (DeltaGFile) {
571 : int backboneflag = 0;
572 23 : while(getline(DeltaGFile, DeltaGline)) {
573 22 : if(!DeltaGline.empty()) {
574 : std::vector<std::string> DeltaGtoken;
575 21 : split(DeltaGline, DeltaGtoken);
576 2541 : for(unsigned i=0; i<natoms; i++) {
577 2520 : if (DeltaGtoken[0].compare(AtomResidueName[1][i])==0 ) {
578 120 : DeltaG[i].push_back (std::atof(DeltaGtoken[1].c_str()));
579 : }
580 : }
581 21 : if (DeltaGtoken[0].compare("BACKBONE")==0 ) {
582 : backboneflag = 1;
583 1 : DeltaG[natoms].push_back (std::atof(DeltaGtoken[1].c_str()));
584 : }
585 21 : }
586 : }
587 1 : if ( backboneflag == 0) error("Cannot find backbone value in Delta G parameters file\n");
588 : }
589 0 : else error("Cannot open DeltaG file");
590 :
591 121 : for(unsigned i=0; i<natoms; i++) {
592 120 : if (DeltaG[i].size()==0 ) {
593 0 : cout << "Delta G value for residue " << AtomResidueName[1][i] << " not found " << endl;
594 0 : error ("missing Delta G parameter\n");
595 : }
596 : }
597 :
598 2 : }
599 :
600 : //computes free energy values for the sidechains and for the backbone, and assigns values to each atom. Only used if sasa_type = TRANSFER, and if no DELTAGFILE is provided. In this case, the free energy values are those describing the effect of temperature, and the program must know if approach 2 or 3 (as described in Arsiccio and Shea, Protein Cold Denaturation in Implicit Solvent Simulations: A Transfer Free Energy Approach, JPCB, 2021) needs to be used to compute them.
601 :
602 0 : void SASA_HASEL::computeDeltaG() {
603 :
604 0 : for(unsigned i=0; i<natoms; i++) {
605 0 : DeltaG[i].clear();
606 : }
607 :
608 : double T;
609 0 : T = plumed.getAtoms().getKbT()/plumed.getAtoms().getKBoltzmann();
610 :
611 0 : if (T != Ti) {
612 0 : for(unsigned i=0; i<natoms; i++) {
613 0 : if (approach==2) {
614 0 : if (AtomResidueName[1][i].compare("ALA")==0) {
615 0 : DeltaG[i].push_back (-2.995/1000*std::pow(T,2)+1.808*T-272.895);
616 : }
617 0 : if (AtomResidueName[1][i].compare("ARG")==0) {
618 0 : DeltaG[i].push_back (-3.182/1000*std::pow(T,2)+1.894*T-282.032);
619 : }
620 0 : if (AtomResidueName[1][i].compare("ASN")==0) {
621 0 : DeltaG[i].push_back (-1.047/1000*std::pow(T,2)+0.6068*T-87.846);
622 : }
623 0 : if (AtomResidueName[1][i].compare("ASP")==0) {
624 0 : DeltaG[i].push_back (-0.1794/1000*std::pow(T,2)+0.1091*T-16.526);
625 : }
626 0 : if (AtomResidueName[1][i].compare("CYS")==0) {
627 0 : DeltaG[i].push_back (-3.09/1000*std::pow(T,2)+1.835*T-272.26);
628 : }
629 0 : if (AtomResidueName[1][i].compare("GLN")==0) {
630 0 : DeltaG[i].push_back (-2.23/1000*std::pow(T,2)+1.335*T-199.707);
631 : }
632 0 : if (AtomResidueName[1][i].compare("GLU")==0) {
633 0 : DeltaG[i].push_back (-1.511/1000*std::pow(T,2)+0.8904*T-131.168);
634 : }
635 0 : if (AtomResidueName[1][i].compare("GLY")==0) {
636 0 : DeltaG[i].push_back (0);
637 : }
638 0 : if (AtomResidueName[1][i].compare("HIS")==0) {
639 0 : DeltaG[i].push_back (-3.482/1000*std::pow(T,2)+2.084*T-311.694);
640 : }
641 0 : if (AtomResidueName[1][i].compare("ILE")==0) {
642 0 : DeltaG[i].push_back (-6.364/1000*std::pow(T,2)+3.8*T-567.444);
643 : }
644 0 : if (AtomResidueName[1][i].compare("LEU")==0) {
645 0 : DeltaG[i].push_back (-7.466/1000*std::pow(T,2)+4.417*T-653.394);
646 : }
647 0 : if (AtomResidueName[1][i].compare("LYS")==0) {
648 0 : DeltaG[i].push_back (-2.091/1000*std::pow(T,2)+1.2458*T-185.549);
649 : }
650 0 : if (AtomResidueName[1][i].compare("MET")==0) {
651 0 : DeltaG[i].push_back (-3.807/1000*std::pow(T,2)+2.272*T-339.007);
652 : }
653 0 : if (AtomResidueName[1][i].compare("PHE")==0) {
654 0 : DeltaG[i].push_back (-7.828/1000*std::pow(T,2)+4.644*T-688.874);
655 : }
656 0 : if (AtomResidueName[1][i].compare("PRO")==0) {
657 0 : DeltaG[i].push_back (-2.347/1000*std::pow(T,2)+1.411*T-212.059);
658 : }
659 0 : if (AtomResidueName[1][i].compare("SER")==0) {
660 0 : DeltaG[i].push_back (1.813/1000*std::pow(T,2)-1.05*T+151.957);
661 : }
662 0 : if (AtomResidueName[1][i].compare("THR")==0) {
663 0 : DeltaG[i].push_back (-2.64/1000*std::pow(T,2)+1.591*T-239.516);
664 : }
665 0 : if (AtomResidueName[1][i].compare("TRP")==0) {
666 0 : DeltaG[i].push_back (-11.66/1000*std::pow(T,2)+6.916*T-1025.293);
667 : }
668 0 : if (AtomResidueName[1][i].compare("TYR")==0) {
669 0 : DeltaG[i].push_back (-7.513/1000*std::pow(T,2)+4.478*T-667.261);
670 : }
671 0 : if (AtomResidueName[1][i].compare("VAL")==0) {
672 0 : DeltaG[i].push_back (-4.902/1000*std::pow(T,2)+2.921*T-435.309);
673 : }
674 0 : DeltaG[natoms].push_back (-0.6962/1000*std::pow(T,2)+0.4426*T-70.015);
675 : }
676 0 : if (approach==3) {
677 0 : if (AtomResidueName[1][i].compare("ALA")==0) {
678 0 : DeltaG[i].push_back (-2.995/1000*std::pow(T,2)+1.808*T-272.105);
679 : }
680 0 : if (AtomResidueName[1][i].compare("ARG")==0) {
681 0 : DeltaG[i].push_back (-3.182/1000*std::pow(T,2)+1.894*T-284.086);
682 : }
683 0 : if (AtomResidueName[1][i].compare("ASN")==0) {
684 0 : DeltaG[i].push_back (-1.047/1000*std::pow(T,2)+0.6068*T-90.597);
685 : }
686 0 : if (AtomResidueName[1][i].compare("ASP")==0) {
687 0 : DeltaG[i].push_back (-0.1794/1000*std::pow(T,2)+0.1091*T-19.143);
688 : }
689 0 : if (AtomResidueName[1][i].compare("CYS")==0) {
690 0 : DeltaG[i].push_back (-3.09/1000*std::pow(T,2)+1.835*T-268.527);
691 : }
692 0 : if (AtomResidueName[1][i].compare("GLN")==0) {
693 0 : DeltaG[i].push_back (-2.23/1000*std::pow(T,2)+1.335*T-201.559);
694 : }
695 0 : if (AtomResidueName[1][i].compare("GLU")==0) {
696 0 : DeltaG[i].push_back (-1.511/1000*std::pow(T,2)+0.8904*T-133.543);
697 : }
698 0 : if (AtomResidueName[1][i].compare("GLY")==0) {
699 0 : DeltaG[i].push_back (0);
700 : }
701 0 : if (AtomResidueName[1][i].compare("HIS")==0) {
702 0 : DeltaG[i].push_back (-3.482/1000*std::pow(T,2)+2.084*T-315.398);
703 : }
704 0 : if (AtomResidueName[1][i].compare("ILE")==0) {
705 0 : DeltaG[i].push_back (-6.364/1000*std::pow(T,2)+3.8*T-564.825);
706 : }
707 0 : if (AtomResidueName[1][i].compare("LEU")==0) {
708 0 : DeltaG[i].push_back (-7.466/1000*std::pow(T,2)+4.417*T-651.483);
709 : }
710 0 : if (AtomResidueName[1][i].compare("LYS")==0) {
711 0 : DeltaG[i].push_back (-2.091/1000*std::pow(T,2)+1.2458*T-187.485);
712 : }
713 0 : if (AtomResidueName[1][i].compare("MET")==0) {
714 0 : DeltaG[i].push_back (-3.807/1000*std::pow(T,2)+2.272*T-339.242);
715 : }
716 0 : if (AtomResidueName[1][i].compare("PHE")==0) {
717 0 : DeltaG[i].push_back (-7.828/1000*std::pow(T,2)+4.644*T-687.134);
718 : }
719 0 : if (AtomResidueName[1][i].compare("PRO")==0) {
720 0 : DeltaG[i].push_back (-2.347/1000*std::pow(T,2)+1.411*T-214.211);
721 : }
722 0 : if (AtomResidueName[1][i].compare("SER")==0) {
723 0 : DeltaG[i].push_back (1.813/1000*std::pow(T,2)-1.05*T+150.289);
724 : }
725 0 : if (AtomResidueName[1][i].compare("THR")==0) {
726 0 : DeltaG[i].push_back (-2.64/1000*std::pow(T,2)+1.591*T-240.267);
727 : }
728 0 : if (AtomResidueName[1][i].compare("TRP")==0) {
729 0 : DeltaG[i].push_back (-11.66/1000*std::pow(T,2)+6.916*T-1024.284);
730 : }
731 0 : if (AtomResidueName[1][i].compare("TYR")==0) {
732 0 : DeltaG[i].push_back (-7.513/1000*std::pow(T,2)+4.478*T-666.484);
733 : }
734 0 : if (AtomResidueName[1][i].compare("VAL")==0) {
735 0 : DeltaG[i].push_back (-4.902/1000*std::pow(T,2)+2.921*T-433.013);
736 : }
737 0 : DeltaG[natoms].push_back (-0.6927/1000*std::pow(T,2)+0.4404*T-68.724);
738 : }
739 : }
740 : }
741 :
742 0 : Ti = T;
743 :
744 0 : if (firstStepFlag ==0) {
745 0 : if (approach!=2 && approach!=3) {
746 0 : cout << "Unknown approach " << approach << endl;
747 : }
748 0 : for(unsigned i=0; i<natoms; i++) {
749 0 : if (DeltaG[i].size()==0 ) {
750 0 : cout << "Delta G value for residue " << AtomResidueName[1][i] << " not found " << endl;
751 0 : error ("missing Delta G parameter\n");
752 : }
753 : }
754 : }
755 0 : }
756 :
757 :
758 : //calculates neighbor list
759 24 : void SASA_HASEL::calcNlist() {
760 24 : if(!nopbc) makeWhole();
761 :
762 2904 : for(unsigned i = 0; i < natoms; i++) {
763 2880 : Nlist[i].clear();
764 : }
765 :
766 2904 : for(unsigned i = 0; i < natoms; i++) {
767 2880 : if (SASAparam[i].size()>0) {
768 103680 : for (unsigned j = 0; j < i; j++) {
769 101952 : if (SASAparam[j].size()>0) {
770 61344 : const Vector Delta_ij_vec = delta( getPosition(i), getPosition(j) );
771 61344 : double Delta_ij_mod = Delta_ij_vec.modulo()*10;
772 61344 : double overlapD = SASAparam[i][0]+SASAparam[j][0];
773 61344 : if (Delta_ij_mod < overlapD) {
774 26748 : Nlist.at(i).push_back (j);
775 26748 : Nlist.at(j).push_back (i);
776 : }
777 : }
778 : }
779 : }
780 : }
781 24 : }
782 :
783 :
784 : //calculates SASA according to Hasel et al., Tetrahedron Computer Methodology Vol. 1, No. 2, pp. 103-116, 1988
785 24 : void SASA_HASEL::calculate() {
786 24 : if(!nopbc) makeWhole();
787 :
788 24 : if(getExchangeStep()) nl_update = 0;
789 24 : if (firstStepFlag ==0) {
790 2 : readPDB();
791 2 : readSASAparam();
792 : }
793 24 : if (nl_update == 0) {
794 24 : calcNlist();
795 : }
796 :
797 :
798 24 : auto* moldat = plumed.getActionSet().selectLatest<GenericMolInfo*>(this);
799 24 : if( ! moldat ) error("Unable to find MOLINFO in input");
800 : double Si, sasai, bij;
801 24 : double sasa = 0;
802 24 : vector<Vector> derivatives( natoms );
803 2904 : for(unsigned i = 0; i < natoms; i++) {
804 2880 : derivatives[i][0] = 0.;
805 2880 : derivatives[i][1] = 0.;
806 2880 : derivatives[i][2] = 0.;
807 : }
808 :
809 24 : Tensor virial;
810 24 : vector <double> ddij_di(3);
811 24 : vector <double> dbij_di(3);
812 24 : vector <double> dAijt_di(3);
813 :
814 24 : if( sasa_type==TOTAL ) {
815 1452 : for(unsigned i = 0; i < natoms; i++) {
816 1440 : if(SASAparam[i].size() > 0) {
817 864 : double ri = SASAparam[i][0];
818 864 : Si = 4*M_PI*ri*ri;
819 : sasai = 1.0;
820 :
821 1728 : vector <vector <double> > derTerm( Nlist[i].size(), vector <double>(3));
822 :
823 864 : dAijt_di[0] = 0;
824 864 : dAijt_di[1] = 0;
825 864 : dAijt_di[2] = 0;
826 864 : int NumRes_i = moldat->getResidueNumber(atoms[i]);
827 :
828 27612 : for (unsigned j = 0; j < Nlist[i].size(); j++) {
829 : double pij = 0.3516;
830 :
831 26748 : int NumRes_j = moldat->getResidueNumber(atoms[Nlist[i][j]]);
832 26748 : if (NumRes_i==NumRes_j) {
833 4320 : if (CONNECTparam[i][0].compare(AtomResidueName[0][Nlist[i][j]])==0 || CONNECTparam[i][1].compare(AtomResidueName[0][Nlist[i][j]])==0 || CONNECTparam[i][2].compare(AtomResidueName[0][Nlist[i][j]])==0 || CONNECTparam[i][3].compare(AtomResidueName[0][Nlist[i][j]])==0) {
834 : pij = 0.8875;
835 : }
836 : }
837 26748 : if ( abs(NumRes_i-NumRes_j) == 1 ) {
838 10380 : if ((AtomResidueName[0][i] == "N" && AtomResidueName[0][Nlist[i][j]]== "CA") || (AtomResidueName[0][Nlist[i][j]] == "N" && AtomResidueName[0][i]== "CA")) {
839 : pij = 0.8875;
840 : }
841 : }
842 :
843 26748 : const Vector d_ij_vec = delta( getPosition(i), getPosition(Nlist[i][j]) );
844 26748 : double d_ij = d_ij_vec.modulo()*10;
845 :
846 26748 : double rj = SASAparam[Nlist[i][j]][0];
847 26748 : bij = M_PI*ri*(ri+rj-d_ij)*(1+(rj-ri)/d_ij); //Angstrom2
848 :
849 26748 : sasai = sasai*(1-SASAparam[i][1]*pij*bij/Si); //nondimensional
850 :
851 26748 : ddij_di[0] = -10*(getPosition(Nlist[i][j])[0]-getPosition(i)[0])/d_ij; //nondimensional
852 26748 : ddij_di[1] = -10*(getPosition(Nlist[i][j])[1]-getPosition(i)[1])/d_ij;
853 26748 : ddij_di[2] = -10*(getPosition(Nlist[i][j])[2]-getPosition(i)[2])/d_ij;
854 :
855 26748 : dbij_di[0] = -M_PI*ri*ddij_di[0]*(1+(ri+rj)*(rj-ri)/(d_ij*d_ij)); //Angstrom
856 26748 : dbij_di[1] = -M_PI*ri*ddij_di[1]*(1+(ri+rj)*(rj-ri)/(d_ij*d_ij));
857 26748 : dbij_di[2] = -M_PI*ri*ddij_di[2]*(1+(ri+rj)*(rj-ri)/(d_ij*d_ij));
858 :
859 26748 : dAijt_di[0] += -1/(Si/(SASAparam[i][1]*pij)-bij)*dbij_di[0]; //Angstrom-1
860 26748 : dAijt_di[1] += -1/(Si/(SASAparam[i][1]*pij)-bij)*dbij_di[1];
861 26748 : dAijt_di[2] += -1/(Si/(SASAparam[i][1]*pij)-bij)*dbij_di[2];
862 :
863 26748 : derTerm[j][0] = 1/(Si/(SASAparam[i][1]*pij)-bij)*dbij_di[0]; //Angstrom-1
864 26748 : derTerm[j][1] = 1/(Si/(SASAparam[i][1]*pij)-bij)*dbij_di[1];
865 26748 : derTerm[j][2] = 1/(Si/(SASAparam[i][1]*pij)-bij)*dbij_di[2];
866 :
867 : }
868 :
869 864 : sasa += Si*sasai/100; //nm2
870 :
871 864 : derivatives[i][0] += Si*sasai/10*dAijt_di[0]; //nm
872 864 : derivatives[i][1] += Si*sasai/10*dAijt_di[1];
873 864 : derivatives[i][2] += Si*sasai/10*dAijt_di[2];
874 :
875 27612 : for (unsigned j = 0; j < Nlist[i].size(); j++) {
876 26748 : derivatives[Nlist[i][j]][0] += Si*sasai/10*derTerm[j][0]; //nm
877 26748 : derivatives[Nlist[i][j]][1] += Si*sasai/10*derTerm[j][1];
878 26748 : derivatives[Nlist[i][j]][2] += Si*sasai/10*derTerm[j][2];
879 : }
880 864 : }
881 : }
882 : }
883 :
884 :
885 24 : if( sasa_type==TRANSFER ) {
886 :
887 12 : if (firstStepFlag ==0) {
888 1 : readMaxSurf();
889 : }
890 :
891 12 : if (firstStepFlag ==0 && DeltaGValues != "absent") {
892 1 : readDeltaG();
893 : }
894 :
895 12 : if (DeltaGValues == "absent") {
896 0 : computeDeltaG();
897 : }
898 :
899 :
900 1452 : for(unsigned i = 0; i < natoms; i++) {
901 :
902 :
903 :
904 1440 : if(SASAparam[i].size() > 0) {
905 864 : double ri = SASAparam[i][0];
906 864 : Si = 4*M_PI*ri*ri;
907 : sasai = 1.0;
908 :
909 1728 : vector <vector <double> > derTerm( Nlist[i].size(), vector <double>(3));
910 :
911 864 : dAijt_di[0] = 0;
912 864 : dAijt_di[1] = 0;
913 864 : dAijt_di[2] = 0;
914 864 : int NumRes_i = moldat->getResidueNumber(atoms[i]);
915 :
916 27612 : for (unsigned j = 0; j < Nlist[i].size(); j++) {
917 : double pij = 0.3516;
918 :
919 26748 : int NumRes_j = moldat->getResidueNumber(atoms[Nlist[i][j]]);
920 26748 : if (NumRes_i==NumRes_j) {
921 4320 : if (CONNECTparam[i][0].compare(AtomResidueName[0][Nlist[i][j]])==0 || CONNECTparam[i][1].compare(AtomResidueName[0][Nlist[i][j]])==0 || CONNECTparam[i][2].compare(AtomResidueName[0][Nlist[i][j]])==0 || CONNECTparam[i][3].compare(AtomResidueName[0][Nlist[i][j]])==0) {
922 : pij = 0.8875;
923 : }
924 : }
925 26748 : if ( abs(NumRes_i-NumRes_j) == 1 ) {
926 10380 : if ((AtomResidueName[0][i] == "N" && AtomResidueName[0][Nlist[i][j]]== "CA") || (AtomResidueName[0][Nlist[i][j]] == "N" && AtomResidueName[0][i]== "CA")) {
927 : pij = 0.8875;
928 : }
929 : }
930 :
931 26748 : const Vector d_ij_vec = delta( getPosition(i), getPosition(Nlist[i][j]) );
932 26748 : double d_ij = d_ij_vec.modulo()*10;
933 :
934 26748 : double rj = SASAparam[Nlist[i][j]][0];
935 26748 : bij = M_PI*ri*(ri+rj-d_ij)*(1+(rj-ri)/d_ij); //Angstrom2
936 :
937 26748 : sasai = sasai*(1-SASAparam[i][1]*pij*bij/Si); //nondimensional
938 :
939 26748 : ddij_di[0] = -10*(getPosition(Nlist[i][j])[0]-getPosition(i)[0])/d_ij; //nondimensional
940 26748 : ddij_di[1] = -10*(getPosition(Nlist[i][j])[1]-getPosition(i)[1])/d_ij;
941 26748 : ddij_di[2] = -10*(getPosition(Nlist[i][j])[2]-getPosition(i)[2])/d_ij;
942 :
943 26748 : dbij_di[0] = -M_PI*ri*ddij_di[0]*(1+(ri+rj)*(rj-ri)/(d_ij*d_ij)); //Angstrom
944 26748 : dbij_di[1] = -M_PI*ri*ddij_di[1]*(1+(ri+rj)*(rj-ri)/(d_ij*d_ij));
945 26748 : dbij_di[2] = -M_PI*ri*ddij_di[2]*(1+(ri+rj)*(rj-ri)/(d_ij*d_ij));
946 :
947 26748 : dAijt_di[0] += -1/(Si/(SASAparam[i][1]*pij)-bij)*dbij_di[0]; //Angstrom-1
948 26748 : dAijt_di[1] += -1/(Si/(SASAparam[i][1]*pij)-bij)*dbij_di[1];
949 26748 : dAijt_di[2] += -1/(Si/(SASAparam[i][1]*pij)-bij)*dbij_di[2];
950 :
951 26748 : derTerm[j][0] = 1/(Si/(SASAparam[i][1]*pij)-bij)*dbij_di[0]; //Angstrom-1
952 26748 : derTerm[j][1] = 1/(Si/(SASAparam[i][1]*pij)-bij)*dbij_di[1];
953 26748 : derTerm[j][2] = 1/(Si/(SASAparam[i][1]*pij)-bij)*dbij_di[2];
954 :
955 : }
956 :
957 2880 : if (AtomResidueName[0][i] == "N" || AtomResidueName[0][i] == "CA" || AtomResidueName[0][i] == "C" || AtomResidueName[0][i] == "O" || AtomResidueName[0][i] == "H") {
958 :
959 720 : sasa += Si*sasai/MaxSurf[i][0]*DeltaG[natoms][0]; //kJ/mol
960 :
961 :
962 720 : derivatives[i][0] += Si*sasai*dAijt_di[0]/MaxSurf[i][0]*DeltaG[natoms][0]*10; //kJ/mol/nm
963 720 : derivatives[i][1] += Si*sasai*dAijt_di[1]/MaxSurf[i][0]*DeltaG[natoms][0]*10;
964 720 : derivatives[i][2] += Si*sasai*dAijt_di[2]/MaxSurf[i][0]*DeltaG[natoms][0]*10;
965 : }
966 :
967 2880 : if (AtomResidueName[0][i] != "N" && AtomResidueName[0][i] != "CA" && AtomResidueName[0][i] != "C" && AtomResidueName[0][i] != "O" && AtomResidueName[0][i] != "H") {
968 144 : sasa += Si*sasai/MaxSurf[i][1]*DeltaG[i][0]; //kJ/mol
969 :
970 144 : derivatives[i][0] += Si*sasai*dAijt_di[0]/MaxSurf[i][1]*DeltaG[i][0]*10; //kJ/mol/nm
971 144 : derivatives[i][1] += Si*sasai*dAijt_di[1]/MaxSurf[i][1]*DeltaG[i][0]*10;
972 144 : derivatives[i][2] += Si*sasai*dAijt_di[2]/MaxSurf[i][1]*DeltaG[i][0]*10;
973 : }
974 :
975 :
976 27612 : for (unsigned j = 0; j < Nlist[i].size(); j++) {
977 86883 : if (AtomResidueName[0][i] == "N" || AtomResidueName[0][i] == "CA" || AtomResidueName[0][i] == "C" || AtomResidueName[0][i] == "O" || AtomResidueName[0][i] == "H") {
978 22438 : derivatives[Nlist[i][j]][0] += Si*sasai*10*derTerm[j][0]/MaxSurf[i][0]*DeltaG[natoms][0]; //kJ/mol/nm
979 22438 : derivatives[Nlist[i][j]][1] += Si*sasai*10*derTerm[j][1]/MaxSurf[i][0]*DeltaG[natoms][0];
980 22438 : derivatives[Nlist[i][j]][2] += Si*sasai*10*derTerm[j][2]/MaxSurf[i][0]*DeltaG[natoms][0];
981 : }
982 :
983 86883 : if (AtomResidueName[0][i] != "N" && AtomResidueName[0][i] != "CA" && AtomResidueName[0][i] != "C" && AtomResidueName[0][i] != "O" && AtomResidueName[0][i] != "H") {
984 4310 : derivatives[Nlist[i][j]][0] += Si*sasai*10*derTerm[j][0]/MaxSurf[i][1]*DeltaG[i][0]; //kJ/mol/nm
985 4310 : derivatives[Nlist[i][j]][1] += Si*sasai*10*derTerm[j][1]/MaxSurf[i][1]*DeltaG[i][0];
986 4310 : derivatives[Nlist[i][j]][2] += Si*sasai*10*derTerm[j][2]/MaxSurf[i][1]*DeltaG[i][0];
987 : }
988 : }
989 864 : }
990 : }
991 : }
992 :
993 :
994 2904 : for(unsigned i=0; i<natoms; i++) {
995 2880 : setAtomsDerivatives(i,derivatives[i]);
996 2880 : virial -= Tensor(getPosition(i),derivatives[i]);
997 : }
998 :
999 24 : setBoxDerivatives(virial);
1000 24 : setValue(sasa);
1001 24 : firstStepFlag = 1;
1002 24 : ++nl_update;
1003 24 : if (nl_update == stride) {
1004 24 : nl_update = 0;
1005 : }
1006 : // setBoxDerivativesNoPbc();
1007 24 : }
1008 :
1009 : }//namespace sasa
1010 : }//namespace PLMD
|
