ADL: Ligand mapping

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ADL: Ligand mapping

Michel Bielecki
Hey everybody,

I am currently trying to compare the binding energies of a known substrate
and one of which we suspect to be the substrate.
When trying to do a mapping using the latter one (G3P) I got this error
message:

Non interal charge on G3P: - 04997
correct 1 residues: G3P1 0.4997
Charges should be corrected in written output file!

Now while I do understand why I am getting this message I do not know what
I have to edit in the pdbqt file - this is the pdbqt in text format:

REMARK  8 active torsions:
REMARK  status: ('A' for Active; 'I' for Inactive)
REMARK    1  A    between atoms: O1_1  and  C1_2
REMARK    2  A    between atoms: C1_2  and  C2_3
REMARK    3  A    between atoms: C2_3  and  O2_4
REMARK    4  A    between atoms: C2_3  and  C3_5
REMARK    5  A    between atoms: C3_5  and  O1P_6
REMARK    6  A    between atoms: O1P_6  and  P_10
REMARK    7  A    between atoms: O4P_7  and  P_10
REMARK    8  A    between atoms: O3P_9  and  P_10
ROOT
ATOM      1  C3  G3P A   1       0.675   0.410   0.291  1.00 10.00
0.214 C
ENDROOT
BRANCH   1   2
ATOM      2  C2  G3P A   1       1.997  -0.105  -0.279  1.00 10.00
0.166 C
BRANCH   2   3
ATOM      3  C1  G3P A   1       3.156   0.705   0.305  1.00 10.00
0.198 C
BRANCH   3   4
ATOM      4  O1  G3P A   1       4.379   0.302  -0.314  1.00 10.00
 -0.398 OA
ATOM      5  HO1 G3P A   1       5.158   0.776   0.009  1.00 10.00
0.209 HD
ENDBRANCH   3   4
ENDBRANCH   2   3
BRANCH   2   6
ATOM      6  O2  G3P A   1       2.159  -1.483   0.064  1.00 10.00
 -0.391 OA
ATOM      7  HO2 G3P A   1       2.174  -1.652   1.016  1.00 10.00
0.210 HD
ENDBRANCH   2   6
ENDBRANCH   1   2
BRANCH   1   8
ATOM      8  O1P G3P A   1      -0.413  -0.267  -0.341  1.00 10.00
 -0.294 OA
BRANCH   8   9
ATOM      9  P   G3P A   1      -1.955   0.027   0.016  1.00 10.00
0.390 P
ATOM     10  O2P G3P A   1      -2.166  -0.144   1.472  1.00 10.00
 -0.632 OA
BRANCH   9  11
ATOM     11  O4P G3P A   1      -2.898  -1.003  -0.786  1.00 10.00
 -0.307 OA
ATOM     12 4HOP G3P A   1      -3.842  -0.884  -0.619  1.00 10.00
0.222 HD
ENDBRANCH   9  11
BRANCH   9  13
ATOM     13  O3P G3P A   1      -2.326   1.535  -0.406  1.00 10.00
 -0.307 OA
ATOM     14 3HOP G3P A   1      -2.212   1.719  -1.349  1.00 10.00
0.222 HD
ENDBRANCH   9  13
ENDBRANCH   8   9
ENDBRANCH   1   8
TORSDOF 8


Can anybody help? Or give a short explanation what and where I have to
change? While I found several tutorials explaining why I have to do it, I
haven´t seen one so far explaining how to do it..

Thanks in advance,

Michael
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Re: ADL: Ligand mapping

Ruth Huey
Using 1-based counting, the partial charges are in columns 67-76 in a pdbqt file.
(The autodock atom type follows in columns 78-79).

SO to adjust the total charge on your ligand pdbqt file, open it in a text editor and change the charge on one or more atoms.
 
   Best wishes,
        Ruth
________________________________________
From: [hidden email] [[hidden email]] On Behalf Of Michel Bielecki [[hidden email]]
Sent: Tuesday, February 25, 2014 2:51 AM
To: [hidden email]
Subject: ADL: Ligand mapping

Hey everybody,

I am currently trying to compare the binding energies of a known substrate
and one of which we suspect to be the substrate.
When trying to do a mapping using the latter one (G3P) I got this error
message:

Non interal charge on G3P: - 04997
correct 1 residues: G3P1 0.4997
Charges should be corrected in written output file!

Now while I do understand why I am getting this message I do not know what
I have to edit in the pdbqt file - this is the pdbqt in text format:

REMARK  8 active torsions:
REMARK  status: ('A' for Active; 'I' for Inactive)
REMARK    1  A    between atoms: O1_1  and  C1_2
REMARK    2  A    between atoms: C1_2  and  C2_3
REMARK    3  A    between atoms: C2_3  and  O2_4
REMARK    4  A    between atoms: C2_3  and  C3_5
REMARK    5  A    between atoms: C3_5  and  O1P_6
REMARK    6  A    between atoms: O1P_6  and  P_10
REMARK    7  A    between atoms: O4P_7  and  P_10
REMARK    8  A    between atoms: O3P_9  and  P_10
ROOT
ATOM      1  C3  G3P A   1       0.675   0.410   0.291  1.00 10.00
0.214 C
ENDROOT
BRANCH   1   2
ATOM      2  C2  G3P A   1       1.997  -0.105  -0.279  1.00 10.00
0.166 C
BRANCH   2   3
ATOM      3  C1  G3P A   1       3.156   0.705   0.305  1.00 10.00
0.198 C
BRANCH   3   4
ATOM      4  O1  G3P A   1       4.379   0.302  -0.314  1.00 10.00
 -0.398 OA
ATOM      5  HO1 G3P A   1       5.158   0.776   0.009  1.00 10.00
0.209 HD
ENDBRANCH   3   4
ENDBRANCH   2   3
BRANCH   2   6
ATOM      6  O2  G3P A   1       2.159  -1.483   0.064  1.00 10.00
 -0.391 OA
ATOM      7  HO2 G3P A   1       2.174  -1.652   1.016  1.00 10.00
0.210 HD
ENDBRANCH   2   6
ENDBRANCH   1   2
BRANCH   1   8
ATOM      8  O1P G3P A   1      -0.413  -0.267  -0.341  1.00 10.00
 -0.294 OA
BRANCH   8   9
ATOM      9  P   G3P A   1      -1.955   0.027   0.016  1.00 10.00
0.390 P
ATOM     10  O2P G3P A   1      -2.166  -0.144   1.472  1.00 10.00
 -0.632 OA
BRANCH   9  11
ATOM     11  O4P G3P A   1      -2.898  -1.003  -0.786  1.00 10.00
 -0.307 OA
ATOM     12 4HOP G3P A   1      -3.842  -0.884  -0.619  1.00 10.00
0.222 HD
ENDBRANCH   9  11
BRANCH   9  13
ATOM     13  O3P G3P A   1      -2.326   1.535  -0.406  1.00 10.00
 -0.307 OA
ATOM     14 3HOP G3P A   1      -2.212   1.719  -1.349  1.00 10.00
0.222 HD
ENDBRANCH   9  13
ENDBRANCH   8   9
ENDBRANCH   1   8
TORSDOF 8


Can anybody help? Or give a short explanation what and where I have to
change? While I found several tutorials explaining why I have to do it, I
haven´t seen one so far explaining how to do it..

Thanks in advance,

Michael
________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---

________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---