You don't need any additional software - you can simply use sed command in bash. It shouldn't take more than 2 seconds to fix the "problem".

Thanks Rafal Jakubowski for your kind suggestion, But I use windows OS. And I have figured out the solution to my problem. Its rather simple. You just need to edit the pdb file in text editor . First of all, I have removed all Hydrogen atoms from my pdb file using SPDBV. This will remove hydrogens from standard aminoacid residues, but do not affect Heteroatoms. Then, I located the extra hydrogen atoms (like HD1, HB1, HB2, HD2 etc) that are not described in traditional PDB format. In traditional PDB convention there are only 10 lines to define a histidine residue and I made sure that only 10 lines corresponding to His (lines for N, CA, C,O,CB, CG, ND1, CD2, CE1 and NE2) are retained in file in the order just described above. If you have to rearrange the lines, then make sure that you appropriately renumber the atoms in second column of PDB file. Then replace all HID (or other 3 letter code) with HIS. Again replace HETATM by ATOM. Do this for remaining histidines in your molecules. save the file and you are ready to go. Just simple as that and it worked!

Here is the part of file with problem

HETATM 129 N HID G 9 34.194 14.009 23.023 1.00 0.00

HETATM 130 CA HID G 9 34.914 14.240 24.299 1.00 0.00

HETATM 131 C HID G 9 36.454 14.283 24.111 1.00 0.00

HETATM 132 O HID G 9 37.020 13.482 23.358 1.00 0.00

HETATM 133 ND1 HID G 9 32.047 13.538 25.839 1.00 0.00

HETATM 134 HD1 HID G 9 32.057 14.504 26.135 1.00 0.00

HETATM 135 CG HID G 9 33.104 12.735 25.456 1.00 0.00

HETATM 136 CB HID G 9 34.560 13.056 25.295 1.00 0.00

HETATM 137 HB1 HID G 9 35.063 12.117 25.064 1.00 0.00

HETATM 138 HB2 HID G 9 34.860 13.473 26.256 1.00 0.00

HETATM 139 NE2 HID G 9 31.188 11.628 25.690 1.00 0.00

HETATM 140 CD2 HID G 9 32.540 11.464 25.358 1.00 0.00

HETATM 141 HD2 HID G 9 33.043 10.527 25.171 1.00 0.00

HETATM 142 CE1 HID G 9 30.912 12.893 25.922 1.00 0.00

HETATM 143 HE1 HID G 9 29.922 13.296 26.078 1.00 0.00

HETATM 144 HN HID G 9 33.346 13.463 23.076 1.00 0.00

HETATM 145 HA HID G 9 34.553 15.160 24.759 1.00 0.00

ATOM 146 HN HID G 9 33.346 13.463 23.076 1.00 99.99

ATOM 147 HA HID G 9 34.553 15.160 24.759 1.00 99.99

ATOM 148 HD1 HID G 9 32.057 14.504 26.135 1.00 99.99

ATOM 149 HB1 HID G 9 35.063 12.117 25.064 1.00 99.99

ATOM 150 HB2 HID G 9 34.860 13.473 26.256 1.00 99.99

ATOM 151 HD2 HID G 9 33.043 10.527 25.171 1.00 99.99

ATOM 152 HE1 HID G 9 29.922 13.296 26.078 1.00 99.99

And here is portion of file file after fixing

ATOM 71 N HIS G 9 34.194 14.009 23.023 1.00 0.00

ATOM 72 CA HIS G 9 34.914 14.240 24.299 1.00 0.00

ATOM 73 C HIS G 9 36.454 14.283 24.111 1.00 0.00

ATOM 74 O HIS G 9 37.020 13.482 23.358 1.00 0.00

ATOM 75 CB HIS G 9 34.560 13.056 25.295 1.00 0.00

ATOM 76 CG HIS G 9 33.104 12.735 25.456 1.00 0.00

ATOM 77 ND1 HIS G 9 32.047 13.538 25.839 1.00 0.00

ATOM 78 CD2 HIS G 9 32.540 11.464 25.358 1.00 0.00

ATOM 79 CE1 HIS G 9 30.912 12.893 25.922 1.00 0.00

ATOM 80 NE2 HIS G 9 31.188 11.628 25.690 1.00 0.00

Just be sure that AutoDock assigns the protonation state correctly to match the structure you simulated.

You can open (as you did) the pdb file with a text editor and perform find/replace HSE by HIS and that's all.

Hi,

I use always the python scripts from mgltools

$mglbin/pythonsh $mgltools/prepare_receptor4.py -r ${Name}.protein.pdb -v -U nphs_lps_waters

Using this command (with "-U nphs_lps_waters" option ) the nonstandard residue names remain, and will not consider as heteroatom.

HTH,

Balazs