&INFO histidine-440 amino acid extracted from catalytic triade. geometry optimization of the hydrogen positions. to convert the pdb coordinates with vi, you can use: %s,^\(ATOM.*HISAX 440 \)\(.*\) 1\.00 0\.00.*,\2 \1, &END &CPMD OPTIMIZE GEOMETRY XYZ HESSIAN UNITY ODIIS NO_RESET=50 5 CONVERGENCE INITIAL 1.0d-5 CONVERGENCE ORBITALS 1.0d-7 CONVERGENCE GEOMETRY 1.0d-3 CONVERGENCE ADAPT 0.02 CONVERGENCE ENERGY 0.05 MAXSTEP 100 STRUCTURE BONDS ANGLES &END &DFT FUNCTIONAL BLYP GC-CUTOFF 5.0E-06 &END &SYSTEM SYMMETRY 8 ANGSTROM CELL ABSOLUTE 6.5 6.9 7.3 0.0 0.0 0.0 DUAL 5.0 CUTOFF 25.0 &END &ATOMS *N_VDB_BLYP.psp FORMATTED LMAX=P 2 3.860 2.270 2.580 ATOM 9 ND1 HISAX 440 1.650 1.970 2.280 ATOM 15 NE2 HISAX 440 *C_VDB_BLYP.psp FORMATTED LMAX=P 5 4.200 5.100 4.630 ATOM 3 CA HISAX 440 3.860 3.630 4.720 ATOM 5 CB HISAX 440 3.170 3.020 3.510 ATOM 8 CG HISAX 440 1.810 2.760 3.420 ATOM 11 CD2 HISAX 440 2.920 1.670 1.830 ATOM 13 CE1 HISAX 440 *H_VDB_BLYP.psp FORMATTED LMAX=S 8 4.940 5.530 5.820 ATOM 1 H HISAX 440 4.770 5.190 3.710 ATOM 4 HA HISAX 440 4.780 3.060 4.850 ATOM 6 HB1 HISAX 440 3.190 3.450 5.570 ATOM 7 HB2 HISAX 440 4.840 2.060 2.530 ATOM 10 HD1 HISAX 440 1.000 3.070 4.060 ATOM 12 HD2 HISAX 440 3.110 1.000 1.000 ATOM 14 HE1 HISAX 440 2.920 5.860 4.220 ATOM 16 H HISAX 440 CONSTRAINTS FIX ATOMS 7 1 2 3 4 5 6 7 END CONSTRAINTS &END