Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2012-2023 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 : #include "SecondaryStructureRMSD.h"
23 : #include "core/ActionRegister.h"
24 : #include "core/PlumedMain.h"
25 :
26 : namespace PLMD {
27 : namespace secondarystructure {
28 :
29 : //+PLUMEDOC COLVAR ANTIBETARMSD
30 : /*
31 : Probe the antiparallel beta sheet content of your protein structure.
32 :
33 : Two protein segments containing three contiguous residues can form an antiparallel beta sheet.
34 : Although if the two segments are part of the same protein chain they must be separated by
35 : a minimum of 2 residues to make room for the turn. This colvar thus generates the set of
36 : all possible six residue sections that could conceivably form an antiparallel beta sheet
37 : and calculates the RMSD distance between the configuration in which the residues find themselves
38 : and an idealized antiparallel beta sheet structure. These distances can be calculated by either
39 : aligning the instantaneous structure with the reference structure and measuring each
40 : atomic displacement or by calculating differences between the set of inter-atomic
41 : distances in the reference and instantaneous structures.
42 :
43 : This colvar is based on the following reference \cite pietrucci09jctc. The authors of
44 : this paper use the set of distances from the anti parallel beta sheet configurations to measure
45 : the number of segments that have an configuration that resembles an anti parallel beta sheet. This is done by calculating
46 : the following sum of functions of the rmsd distances:
47 :
48 : \f[
49 : s = \sum_i \frac{ 1 - \left(\frac{r_i-d_0}{r_0}\right)^n } { 1 - \left(\frac{r_i-d_0}{r_0}\right)^m }
50 : \f]
51 :
52 : where the sum runs over all possible segments of antiparallel beta sheet. By default the
53 : NN, MM and D_0 parameters are set equal to those used in \cite pietrucci09jctc. The R_0
54 : parameter must be set by the user - the value used in \cite pietrucci09jctc was 0.08 nm.
55 :
56 : If you change the function in the above sum you can calculate quantities such as the average
57 : distance from a purely configuration composed of pure anti-parallel beta sheets or the distance between the set of
58 : residues that is closest to an anti-parallel beta sheet and the reference configuration. To do these sorts of
59 : calculations you can use the AVERAGE and MIN keywords. In addition you can use the LESS_THAN
60 : keyword if you would like to change the form of the switching function. If you use any of these
61 : options you no longer need to specify NN, R_0, MM and D_0.
62 :
63 : Please be aware that for codes like gromacs you must ensure that plumed
64 : reconstructs the chains involved in your CV when you calculate this CV using
65 : anything other than TYPE=DRMSD. For more details as to how to do this see \ref WHOLEMOLECULES.
66 :
67 : \par Examples
68 :
69 : The following input calculates the number of six residue segments of
70 : protein that are in an antiparallel beta sheet configuration.
71 :
72 : \plumedfile
73 : #SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb
74 : MOLINFO STRUCTURE=beta.pdb
75 : ab: ANTIBETARMSD RESIDUES=all STRANDS_CUTOFF=1
76 : \endplumedfile
77 :
78 : Here the same is done use RMSD instead of DRMSD
79 :
80 : \plumedfile
81 : #SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb
82 : MOLINFO STRUCTURE=helix.pdb
83 : WHOLEMOLECULES ENTITY0=1-100
84 : hh: ANTIBETARMSD RESIDUES=all TYPE=OPTIMAL R_0=0.1 STRANDS_CUTOFF=1
85 : \endplumedfile
86 : */
87 : //+ENDPLUMEDOC
88 :
89 : class AntibetaRMSD : public SecondaryStructureRMSD {
90 : public:
91 : static void registerKeywords( Keywords& keys );
92 : explicit AntibetaRMSD(const ActionOptions&);
93 : };
94 :
95 13827 : PLUMED_REGISTER_ACTION(AntibetaRMSD,"ANTIBETARMSD")
96 :
97 25 : void AntibetaRMSD::registerKeywords( Keywords& keys ) {
98 25 : SecondaryStructureRMSD::registerKeywords( keys );
99 50 : keys.add("compulsory","STYLE","all","Antiparallel beta sheets can either form in a single chain or from a pair of chains. If STYLE=all all "
100 : "chain configuration with the appropriate geometry are counted. If STYLE=inter "
101 : "only sheet-like configurations involving two chains are counted, while if STYLE=intra "
102 : "only sheet-like configurations involving a single chain are counted");
103 25 : keys.use("STRANDS_CUTOFF");
104 25 : }
105 :
106 21 : AntibetaRMSD::AntibetaRMSD(const ActionOptions&ao):
107 : Action(ao),
108 21 : SecondaryStructureRMSD(ao) {
109 : // read in the backbone atoms
110 : std::vector<unsigned> chains;
111 42 : readBackboneAtoms( "protein", chains );
112 :
113 : bool intra_chain(false), inter_chain(false);
114 : std::string style;
115 42 : parse("STYLE",style);
116 21 : if( style=="all" ) {
117 : intra_chain=true;
118 : inter_chain=true;
119 3 : } else if( style=="inter") {
120 : intra_chain=false;
121 : inter_chain=true;
122 1 : } else if( style=="intra") {
123 : intra_chain=true;
124 : inter_chain=false;
125 : } else {
126 0 : error( style + " is not a valid directive for the STYLE keyword");
127 : }
128 :
129 : // Align the atoms based on the positions of these two atoms
130 21 : setAtomsFromStrands( 6, 21 );
131 :
132 : // This constructs all conceivable sections of antibeta sheet in the backbone of the chains
133 21 : if( intra_chain ) {
134 : unsigned nprevious=0;
135 19 : std::vector<unsigned> nlist(30);
136 344 : for(unsigned i=0; i<chains.size(); ++i) {
137 325 : if( chains[i]<40 ) {
138 0 : error("segment of backbone is not long enough to form an antiparallel beta hairpin. Each backbone fragment must contain a minimum of 8 residues");
139 : }
140 : // Loop over all possible triples in each 8 residue segment of protein
141 325 : unsigned nres=chains[i]/5;
142 325 : if( chains[i]%5!=0 ) {
143 0 : error("backbone segment received does not contain a multiple of five residues");
144 : }
145 654 : for(unsigned ires=0; ires<nres-7; ires++) {
146 668 : for(unsigned jres=ires+7; jres<nres; jres++) {
147 5424 : for(unsigned k=0; k<15; ++k) {
148 5085 : nlist[k]=nprevious + ires*5+k;
149 5085 : nlist[k+15]=nprevious + (jres-2)*5+k;
150 : }
151 339 : addColvar( nlist );
152 : }
153 : }
154 325 : nprevious+=chains[i];
155 : }
156 : }
157 21 : if( inter_chain ) {
158 21 : if( chains.size()==1 && style!="all" ) {
159 0 : error("there is only one chain defined so cannot use inter_chain option");
160 : }
161 20 : std::vector<unsigned> nlist(30);
162 311 : for(unsigned ichain=1; ichain<chains.size(); ++ichain) {
163 : unsigned iprev=0;
164 2894 : for(unsigned i=0; i<ichain; ++i) {
165 2603 : iprev+=chains[i];
166 : }
167 291 : unsigned inres=chains[ichain]/5;
168 291 : if( chains[ichain]%5!=0 ) {
169 0 : error("backbone segment received does not contain a multiple of five residues");
170 : }
171 2027 : for(unsigned ires=0; ires<inres-2; ++ires) {
172 17344 : for(unsigned jchain=0; jchain<ichain; ++jchain) {
173 : unsigned jprev=0;
174 98840 : for(unsigned i=0; i<jchain; ++i) {
175 83232 : jprev+=chains[i];
176 : }
177 15608 : unsigned jnres=chains[jchain]/5;
178 15608 : if( chains[jchain]%5!=0 ) {
179 0 : error("backbone segment received does not contain a multiple of five residues");
180 : }
181 109246 : for(unsigned jres=0; jres<jnres-2; ++jres) {
182 1498208 : for(unsigned k=0; k<15; ++k) {
183 1404570 : nlist[k]=iprev+ ires*5+k;
184 1404570 : nlist[k+15]=jprev+ jres*5+k;
185 : }
186 93638 : addColvar( nlist );
187 : }
188 : }
189 : }
190 : }
191 : }
192 :
193 : // Build the reference structure ( in angstroms )
194 21 : std::vector<Vector> reference(30);
195 21 : reference[0]=Vector( 2.263, -3.795, 1.722); // N i
196 21 : reference[1]=Vector( 2.493, -2.426, 2.263); // CA
197 21 : reference[2]=Vector( 3.847, -1.838, 1.761); // CB
198 21 : reference[3]=Vector( 1.301, -1.517, 1.921); // C
199 21 : reference[4]=Vector( 0.852, -1.504, 0.739); // O
200 21 : reference[5]=Vector( 0.818, -0.738, 2.917); // N i+1
201 21 : reference[6]=Vector(-0.299, 0.243, 2.748); // CA
202 21 : reference[7]=Vector(-1.421, -0.076, 3.757); // CB
203 21 : reference[8]=Vector( 0.273, 1.680, 2.854); // C
204 21 : reference[9]=Vector( 0.902, 1.993, 3.888); // O
205 21 : reference[10]=Vector( 0.119, 2.532, 1.813); // N i+2
206 21 : reference[11]=Vector( 0.683, 3.916, 1.680); // CA
207 21 : reference[12]=Vector( 1.580, 3.940, 0.395); // CB
208 21 : reference[13]=Vector(-0.394, 5.011, 1.630); // C
209 21 : reference[14]=Vector(-1.459, 4.814, 0.982); // O
210 21 : reference[15]=Vector(-2.962, 3.559, -1.359); // N j-2
211 21 : reference[16]=Vector(-2.439, 2.526, -2.287); // CA
212 21 : reference[17]=Vector(-1.189, 3.006, -3.087); // CB
213 21 : reference[18]=Vector(-2.081, 1.231, -1.520); // C
214 21 : reference[19]=Vector(-1.524, 1.324, -0.409); // O
215 21 : reference[20]=Vector(-2.326, 0.037, -2.095); // N j-1
216 21 : reference[21]=Vector(-1.858, -1.269, -1.554); // CA
217 21 : reference[22]=Vector(-3.053, -2.199, -1.291); // CB
218 21 : reference[23]=Vector(-0.869, -1.949, -2.512); // C
219 21 : reference[24]=Vector(-1.255, -2.070, -3.710); // O
220 21 : reference[25]=Vector( 0.326, -2.363, -2.072); // N j
221 21 : reference[26]=Vector( 1.405, -2.992, -2.872); // CA
222 21 : reference[27]=Vector( 2.699, -2.129, -2.917); // CB
223 21 : reference[28]=Vector( 1.745, -4.399, -2.330); // C
224 21 : reference[29]=Vector( 1.899, -4.545, -1.102); // O
225 :
226 : // Store the secondary structure ( last number makes sure we convert to internal units nm )
227 21 : setSecondaryStructure( reference, 0.17/atoms.getUnits().getLength(), 0.1/atoms.getUnits().getLength() );
228 21 : }
229 :
230 : }
231 : }
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