1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
|
// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
#include <BALL/MOLMEC/AMBER/amber.h>
#include <BALL/STRUCTURE/fragmentDB.h>
#include <BALL/ENERGY/atomicContactEnergy.h>
#include <BALL/ENERGY/coulomb.h>
#include <BALL/FORMAT/PDBFile.h>
#include <BALL/FORMAT/commandlineParser.h>
#include "version.h"
using namespace std;
using namespace BALL;
int main(int argc, char* argv[])
{
// instantiate CommandlineParser object
CommandlineParser parpars("CalculateBindingFreeEnergy", "calculate binding energy of two proteins using AMBER", VERSION, String(__DATE__), "ForceFields");
parpars.registerMandatoryInputFile("pdb_a", "first input pdb file ");
parpars.registerMandatoryInputFile("pdb_b", "second input pdb file ");
///TODO: generate an output file with the energy that is being calculated!!! stdout is not enough!!!
// the manual
String man = String("This tool computes the binding energy of two given pdb files using the AMBER force field.");
parpars.setToolManual(man);
parpars.setSupportedFormats("pdb_a", "pdb");
parpars.setSupportedFormats("pdb_b", "pdb");
// parse the command line
parpars.parse(argc, argv);
PDBFile pdb_a;
pdb_a.open(parpars.get("pdb_a"), std::ios::in);
if (!pdb_a)
{
// if file does not exist: complain and abort
Log.error() << "error opening " << parpars.get("pdb_a") << " for input." << std::endl;
exit(2);
}
PDBFile pdb_b;
pdb_b.open(parpars.get("pdb_b"), std::ios::in);
if (!pdb_b)
{
// if file does not exist: complain and abort
Log.error() << "error opening " << parpars.get("pdb_b") << " for output." << std::endl;
exit(2);
}
// read the contents of the file A into a system
System A;
pdb_a >> A;
pdb_a.close();
// read the contents of the file B into a system
System B;
pdb_b >> B;
pdb_b.close();
// normalize the names and build all bonds
FragmentDB db("");
A.apply(db.normalize_names);
A.apply(db.build_bonds);
B.apply(db.normalize_names);
B.apply(db.build_bonds);
// TODO: Ask ResidueChecker if everything is ok!
// calculate the atomic contact energies of A and B
// NOTE: these methods use BALL internal parameter files
float ACE_A = calculateACE(A);
float ACE_B = calculateACE(B);
// calculate the electrostatic energies of A and B
AmberFF amber;
amber.options[AmberFF::Option::ASSIGN_CHARGES] = true;
amber.options[AmberFF::Option::OVERWRITE_CHARGES] = true;
amber.setup(A);
amber.updateEnergy();
float ES_A = amber.getESEnergy();
float C_A = calculateCoulomb(A);
amber.setup(B);
amber.updateEnergy();
float ES_B = amber.getESEnergy();
float C_B = calculateCoulomb(B);
// finally, join the to systems into a single system
Log << "atoms in A: " << A.countAtoms() << endl;
Log << "atoms in B: " << B.countAtoms() << endl;
A.splice(B);
Log << "final atoms: " << A.countAtoms() << endl;
Log << "======================" << endl;
float ACE_AB = calculateACE(A);
amber.setup(A);
amber.updateEnergy();
float ES_AB = amber.getESEnergy();
float C_AB = calculateCoulomb(A);
// print the resulting energies
Log << "ES energy of A: " << ES_A << endl;
Log << "ES energy of B: " << ES_B << endl;
Log << "ES energy of AB:" << ES_AB << endl;
Log << "C energy of A: " << C_A << endl;
Log << "C energy of B: " << C_B << endl;
Log << "C energy of AB:" << C_AB << endl;
Log << "======================" << endl;
Log << "change in atomic contact energy on binding: "
<< (ACE_AB - ACE_A - ACE_B) << " kJ/mol" << endl;
Log << "change in electrostatic energy on binding: "
<< (ES_AB - ES_A - ES_B) << " kJ/mol" << endl;
Log << "total binding free energy: "
<< (ACE_AB - ACE_A - ACE_B) + (ES_AB - ES_A - ES_B) << " kJ/mol" << endl;
// done
return 0;
}
|
