In the current version of the program, the PDB file with coordinates of atoms in a protein in the input data. The coordinates may be retrieved from the file or PDB database. For computation, indicate the chain identifier, given in the PDB file.
The program automatically prepares the file with topology of the molecule, containing AMBER force field parameters. The program uses this file in further calculations of molecular mechanical minimization. A standard AMBER and/or user topology database of individual residues is used for creating this topology file. AMBER parameters file is used for determining the constants of potential energy function, such as equilibrium bond lengths, angles, dihedral angles, their force constants, non-bonded 6-12 parameters, and H-bond 10-12 parameters.
Minimization stops after 50 iterations.
Program is provided with viewer.
The output data are the coordinates of the atoms of protein chain after minimization in PDB format.
Output example:
HEADER SoftBerry molecular mechanic Ver. 1.0 REMARK 1 REMARK 1 Charge modification is NOT performed. REMARK 1 NO periodic boundaries are applied. REMARK 1 Non-bonded interactions evaluated normally. REMARK 1 Energy is reported in Kcal/mol REMARK 1 Complete interaction is calculated. REMARK 1 NB pairlist generated in residue-residue basis. REMARK 1 No pair list will be generated. REMARK 1 NB list updated every 10 steps. REMARK 1 Buffer region updates every 1 steps. REMARK 1 Constant dielectric function used. REMARK 1 Solvent pointer = 142. REMARK 1 No water model chosen. REMARK 1 NB cutoff distance = 8.0000 Angstroms. REMARK 1 1,4 non-bonds divided by 2.0000. REMARK 1 1,4 electrostatics divided by 2.0000. REMARK 1 The dielectric constant = 1.0000. REMARK 1 The buffer cutoff is 8.00000 Angstroms. REMARK 1 CAP Option is inactivated. REMARK 1 REMARK 1 The number of degrees of freedom = 6426. REMARK 1 INITIAL CONDITIONS OF SYSTEM: REMARK 1 REMARK 1 Potential Energy = -4643.602515 REMARK 1 Non-bond = -784.604532 REMARK 1 H-bond = 0.000000 REMARK 1 Electrostatic = -10490.096084 REMARK 1 Bond = 183.712294 REMARK 1 Angle = 715.484007 REMARK 1 Dihedral = 557.877658 REMARK 1 1,4 Non-bonded = 721.197306 REMARK 1 1,4 Electrostatic= 4452.826836 REMARK 1 REMARK 1 MINIMIZATION TERMINATED : Exceeded maximum number of cycles REMARK 1 Number of function calls 102 REMARK 1 Number of iterations 50 REMARK 1 REMARK 1 Potential Energy = -6031.148428 REMARK 1 Non-bond = -1078.280106 REMARK 1 H-bond = 0.000000 REMARK 1 Electrostatic = -10870.756945 REMARK 1 Bond = 38.980831 REMARK 1 Angle = 364.506930 REMARK 1 Dihedral = 569.815489 REMARK 1 1,4 Non-bonded = 499.520121 REMARK 1 1,4 Electrostatic= 4445.065252 REMARK 1 ATOM 1 N VAL 1 7.357 18.204 5.000 0.058 0.00 ATOM 2 H1 VAL 1 7.744 18.600 5.855 0.227 0.00 ATOM 3 H2 VAL 1 6.358 18.336 4.957 0.227 0.00 ATOM 4 H3 VAL 1 7.576 17.220 4.974 0.227 0.00 ATOM 5 CA VAL 1 7.948 18.857 3.812 -0.005 0.00 ATOM 6 HA VAL 1 7.513 18.373 2.927 0.109 0.00 ATOM 7 CB VAL 1 7.562 20.374 3.761 0.320 0.00 ATOM 8 HB VAL 1 8.205 20.922 4.460 -0.022 0.00 ATOM 9 CG1 VAL 1 7.734 20.963 2.351 -0.313 0.00 ATOM 10 HG1 VAL 1 7.200 20.370 1.614 0.073 0.00 ATOM 11 HG1 VAL 1 7.348 21.971 2.334 0.073 0.00 ATOM 12 HG1 VAL 1 8.777 21.031 2.074 0.073 0.00 ATOM 13 CG2 VAL 1 6.091 20.612 4.182 -0.313 0.00 ATOM 14 HG2 VAL 1 5.914 20.395 5.230 0.073 0.00 ATOM 15 HG2 VAL 1 5.837 21.655 4.045 0.073 0.00 ATOM 16 HG2 VAL 1 5.401 20.033 3.576 0.073 0.00 ATOM 17 C VAL 1 9.470 18.591 3.816 0.616 0.00 ATOM 18 O VAL 1 9.994 18.012 4.791 -0.572 0.00 ATOM 19 N LEU 2 10.152 18.988 2.739 -0.416 0.00 ATOM 20 H LEU 2 9.702 19.420 1.936 0.272 0.00 ATOM 21 CA LEU 2 11.603 19.008 2.683 -0.052 0.00 ATOM 22 HA LEU 2 11.983 18.097 3.120 0.092 0.00 ATOM 23 CB LEU 2 12.095 19.097 1.232 -0.110 0.00 ATOM 24 HB2 LEU 2 11.708 20.020 0.810 0.046 0.00 ….. ….. ….. ATOM 2114 CD2 TYR 140 -4.256 9.053 -10.416 -0.191 0.00 ATOM 2115 HD2 TYR 140 -5.071 8.446 -10.050 0.170 0.00 ATOM 2116 C TYR 140 -7.480 12.287 -10.110 0.597 0.00 ATOM 2117 O TYR 140 -8.121 11.618 -10.920 -0.568 0.00 ATOM 2118 N ARG 141 -8.048 12.955 -9.114 -0.348 0.00 ATOM 2119 H ARG 141 -7.526 13.520 -8.446 0.276 0.00 ATOM 2120 CA ARG 141 -9.462 13.123 -8.845 -0.307 0.00 ATOM 2121 HA ARG 141 -9.978 13.465 -9.741 0.145 0.00 ATOM 2122 CB ARG 141 -10.109 11.835 -8.298 -0.037 0.00 ATOM 2123 HB2 ARG 141 -11.111 12.088 -7.947 0.037 0.00 ATOM 2124 HB3 ARG 141 -10.206 11.103 -9.099 0.037 0.00 ATOM 2125 CG ARG 141 -9.316 11.209 -7.137 0.074 0.00 ATOM 2126 HG2 ARG 141 -8.389 10.775 -7.516 0.018 0.00 ATOM 2127 HG3 ARG 141 -9.057 11.977 -6.410 0.018 0.00 ATOM 2128 CD ARG 141 -10.113 10.122 -6.411 0.111 0.00 ATOM 2129 HD2 ARG 141 -11.122 10.491 -6.222 0.047 0.00 ATOM 2130 HD3 ARG 141 -10.167 9.231 -7.040 0.047 0.00 ATOM 2131 NE ARG 141 -9.476 9.806 -5.122 -0.556 0.00 ATOM 2132 HE ARG 141 -8.628 10.338 -4.986 0.348 0.00 ATOM 2133 CZ ARG 141 -9.989 9.061 -4.137 0.837 0.00 ATOM 2134 NH1 ARG 141 -11.125 8.390 -4.322 -0.874 0.00 ATOM 2135 HH1 ARG 141 -11.567 7.834 -3.606 0.449 0.00 ATOM 2136 HH1 ARG 141 -11.600 8.467 -5.211 0.449 0.00 ATOM 2137 NH2 ARG 141 -9.357 8.998 -2.966 -0.874 0.00 ATOM 2138 HH2 ARG 141 -9.719 8.469 -2.187 0.449 0.00 ATOM 2139 HH2 ARG 141 -8.518 9.540 -2.806 0.449 0.00 ATOM 2140 C ARG 141 -9.530 14.235 -7.814 0.856 0.00 ATOM 2141 O ARG 141 -8.516 14.373 -7.084 -0.826 0.00 ATOM 2142 OXT ARG 141 -10.586 14.879 -7.753 -0.826 0.00