After using the DockPrep tool for Chimera,the following error code is shown (it has the same template but is different for my other proteins) : 

Non-standard atom names:Non-standard atom names: PRO H (PRO 45.A H, PRO 45.A H, PRO 45.A H + 25 others)Total charge for #0: 190.795The following residues had non-integral charges: MET 1.A 1.7458 LEU 2.A 2.719 GLY 3.A 0.5438 THR 4.A 1.6314 ARG 5.A 4.2964 LEU 6.A 2.719 LYS 7.A 4.2964 ALA 8.A 1.0876 ALA 9.A 1.0876 ARG 10.A 4.2964 ILE 11.A 2.719 ARG 12.A 4.2964 ALA 13.A 1.0876 GLY 14.A 0.5438 TYR 15.A 2.1752 SER 16.A 1.0876 GLN 17.A 1.9033 LYS 18.A 4.2964 GLN 19.A 1.9033 LEU 20.A 2.719 GLY 21.A 0.5438 MET 22.A 2.1752 LEU 23.A 2.719 VAL 24.A 2.1752 GLY 25.A 0.5438 MET 26.A 2.1752 ASP 27.A -0.1192 GLU 28.A 0.468 PHE 29.A 2.1752 SER 30.A 1.0876 ALA 31.A 1.0876 SER 32.A 1.0876 ALA 33.A 1.0876 ARG 34.A 4.2964 MET 35.A 2.1752 ASN 36.A 1.3595 GLN 37.A 1.9033 TYR 38.A 2.1752 GLU 39.A 0.468 ARG 40.A 4.2964 GLU 41.A 0.468 ARG 42.A 4.2964 HIS 43.A 1.6314 SER 44.A 1.0876 PRO 45.A -0.2355 ASN 46.A 1.3595 MET 47.A 2.1752 ARG 48.A 4.2964 THR 49.A 1.6314 SER 50.A 1.0876 GLU 51.A 0.468 GLN 52.A 1.9033 LEU 53.A 2.719 ALA 54.A 1.0876 MET 55.A 2.1752 VAL 56.A 2.1752 LEU 57.A 2.719 GLN 58.A 1.9033 VAL 59.A 2.1752 PRO 60.A -0.2355 MET 61.A 2.1752 ALA 62.A 1.0876 TYR 63.A 2.1752 LEU 64.A 2.719 TYR 65.A 2.1752 CYS 66.A 1.0876 PRO 67.A -0.2355 GLU 68.A 0.468 ASP 69.A -0.1192 GLU 70.A 0.468 LEU 71.A 2.719 ALA 72.A 1.0876 GLU 73.A 0.468 LEU 74.A 2.719 ILE 75.A 2.719 LEU 76.A 2.719 LYS 77.A 4.2964 VAL 78.A 2.1752 SER 79.A 1.0876 SER 80.A 1.0876 LEU 81.A 2.719 THR 82.A 1.6314 PRO 83.A -0.2355 GLU 84.A 0.468 PHE 85.A 2.1752 LYS 86.A 4.2964 LYS 87.A 4.2964 GLU 88.A 0.468 LEU 89.A 2.719 THR 90.A 1.6314 ARG 91.A 4.2964 PHE 92.A 2.1752 ILE 93.A 2.719 GLU 94.A 0.468 GLN 95.A 1.9033 LEU 96.A 2.719 LEU 97.A 2.719 ALA 98.A 1.0876 ALA 99.A 1.0876 GLN 100.A 1.9033 GLY 101.A 0.5438

I didn't know that this was a big deal and continued to PyRx but some of my proteins work in Vina Wizard and some don't. I have already googled it and apparently this is about a lot more amino acids than I can fix using the guidelines provided by chimera's website. Is there a tool or a software that helps me fix all of them automatically? Thank you all for answering in advance.