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PostPosted: Thu Jan 14, 2016 10:04 pm 
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Joined: Fri Apr 19, 2013 2:04 pm
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Hi,
I'd like to know what does mean the two last columns in pdbqt files. Specially the final two letters.

Exemple 1:
ATOM 670 N ASP A 72 -4.176 68.684 69.766 1.00 29.24 -0.337 N
ATOM 671 HN ASP A 72 -4.008 69.044 68.827 1.00 0.00 0.164 HD
ATOM 672 CA ASP A 72 -3.139 68.862 70.777 1.00 26.50 0.170 C
ATOM 673 C ASP A 72 -3.611 69.862 71.829 1.00 33.60 0.251 C
ATOM 674 O ASP A 72 -3.873 71.022 71.523 1.00 34.30 -0.271 OA
ATOM 675 CB ASP A 72 -1.860 69.381 70.110 1.00 24.64 0.129 C
ATOM 676 CG ASP A 72 -0.650 69.363 71.035 1.00 24.68 0.188 C
ATOM 677 OD1 ASP A 72 -0.737 69.843 72.184 1.00 27.15 -0.647 OA
ATOM 678 OD2 ASP A 72 0.413 68.884 70.596 1.00 27.37 -0.647 OA

Exemple 2:
ATOM 908 CD1 TYR A 96 -13.347 70.377 51.445 1.00 17.02 -0.002 A

Thanks
Renata


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PostPosted: Mon Jan 18, 2016 8:41 pm 
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For each line in a pdbqt file that starts with ATOM or HETATM the last two columns contain:
(1) the partial charge on that atom
(2) the atom's autodock_element.

examples:
#the first line defines a nitrogen with -0.337 partial charge and autodock_element N
ATOM 670 N ASP A 72 -4.176 68.684 69.766 1.00 29.24 -0.337 N
#this line defines a hydrogen with 0.164 partial charge and autodock_element HD
ATOM 671 HN ASP A 72 -4.008 69.044 68.827 1.00 0.00 0.164 HD


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