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 Post subject: A small help
PostPosted: Mon Aug 26, 2013 4:59 pm 
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Joined: Tue Mar 06, 2012 7:15 pm
Posts: 22
Hi
I did flexible docking with Vina. Then I converted the outputfile (ligand001_out.pdbqt) to .pdb and added the first model to the end part of the rigid coordinate file(rigid.pdb) to form the entire complex having the docked pose of the ligand alongside the flexible residues(complex.pdb).

However I don't see the ligand information in the output file after the flexible docking. I only see the information on the flexible residues.

Thus may I ask how to incorporate the rigid ,flexible part and the docked ligand into a single file.
An example file of the complex would be great.
Also If I can open the complex file in pymol and then mark the ligand, flexible residues and the protein in 3 different colors.

Will greatly appreciate any help or suggestions.

Best
saharinku


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 Post subject: Re: A small help
PostPosted: Fri Aug 30, 2013 5:25 pm 
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Create the file you want by using a text editor to append "rigid.pdbqt" to the end of "Ligand001_out.pdbqt".

Your output file "Ligand001_out.pdbqt" already contains the nine atom ligand along with sidechains of the seven flexible residues (see below): THR103,ARG155,LYS173,GLU245,ASP,246,ASP269,ASN4540

You can visualize this result in AutoDockTools:
-Analyze->Dockings->Open AutoDock vina result...
-Analyze->Macromolecule->Open...

MODEL 1
REMARK VINA RESULT: -4.9 0.000 0.000
REMARK 3 active torsions:
REMARK status: ('A' for Active; 'I' for Inactive)
REMARK 1 A between atoms: C1_1 and C2_2
REMARK 2 A between atoms: C1_1 and C3_4
REMARK 3 A between atoms: C1_1 and O3_6
ROOT
ATOM 1 C1 <0> d 9.973 5.046 -5.019 0.00 0.00 0.320 C
ENDROOT
BRANCH 1 2
ATOM 2 C2 <0> d 9.328 3.714 -5.306 0.00 0.00 0.214 C
ATOM 3 O1 <0> d 9.426 3.220 -6.405 0.00 0.00 -0.646 OA
ATOM 4 O4 <0> d 8.647 3.076 -4.342 0.00 0.00 -0.646 OA
ENDBRANCH 1 2
BRANCH 1 5
ATOM 5 C3 <0> d 11.327 4.826 -4.396 0.00 0.00 0.214 C
ATOM 6 O2 <0> d 12.066 5.763 -4.208 0.00 0.00 -0.646 OA
ATOM 7 O5 <0> d 11.713 3.587 -4.050 0.00 0.00 -0.646 OA
ENDBRANCH 1 5
BRANCH 1 8
ATOM 8 O3 <0> d 10.123 5.776 -6.238 0.00 0.00 -0.375 OA
ATOM 9 H2 <0> d 9.420 5.615 -6.882 0.00 0.00 0.211 HD
ENDBRANCH 1 8
TORSDOF 3

BEGIN_RES THR C 103
REMARK 2 active torsions:
REMARK status: ('A' for Active; 'I' for Inactive)
REMARK 1 A between atoms: CB and OG1
REMARK 2 A between atoms: CA and CB
ROOT
ATOM 1 CA THR C 103 12.713 3.036 -9.887 1.00 50.00 0.187 C
ENDROOT
BRANCH 1 2
ATOM 2 CB THR C 103 11.873 3.185 -8.580 1.00 50.00 0.140 C
ATOM 3 CG2 THR C 103 12.638 2.673 -7.328 1.00 50.00 0.034 C
BRANCH 2 4
ATOM 4 OG1 THR C 103 11.525 4.565 -8.373 1.00 50.00 -0.382 OA
ATOM 5 HG1 THR C 103 10.627 4.685 -8.084 1.00 0.00 0.210 HD
ENDBRANCH 2 4
ENDBRANCH 1 2
END_RES THR C 103
BEGIN_RES ARG C 155
REMARK 4 active torsions:
REMARK status: ('A' for Active; 'I' for Inactive)
REMARK 3 A between atoms: CA and CB
REMARK 4 A between atoms: CB and CG
REMARK 5 A between atoms: CG and CD
REMARK 6 A between atoms: CD and NE
REMARK I between atoms: NE and CZ
REMARK I between atoms: CZ and NH2
REMARK I between atoms: CZ and NH1
ROOT
ATOM 6 CA ARG C 155 10.618 -6.291 -1.013 1.00 50.00 0.159 C
ENDROOT
BRANCH 6 7
ATOM 7 CB ARG C 155 10.011 -5.603 0.241 1.00 50.00 0.034 C
BRANCH 7 8
ATOM 8 CG ARG C 155 8.476 -5.369 0.089 1.00 50.00 0.027 C
BRANCH 8 9
ATOM 9 CD ARG C 155 8.089 -3.866 0.179 1.00 50.00 0.116 C
BRANCH 9 10
ATOM 10 NE ARG C 155 8.834 -3.179 1.240 1.00 50.00 -0.212 N
ATOM 11 CZ ARG C 155 9.673 -2.189 1.019 1.00 50.00 0.666 C
ATOM 12 NH2 ARG C 155 10.319 -1.671 2.039 1.00 50.00 -0.235 N
ATOM 13 NH1 ARG C 155 9.898 -1.698 -0.178 1.00 50.00 -0.235 N
ATOM 14 1HH2 ARG C 155 10.177 -2.023 2.998 1.00 0.00 0.174 HD
ATOM 15 2HH2 ARG C 155 10.990 -0.899 1.910 1.00 0.00 0.174 HD
ATOM 16 1HH1 ARG C 155 9.419 -2.062 -1.012 1.00 0.00 0.174 HD
ATOM 17 2HH1 ARG C 155 10.565 -0.923 -0.316 1.00 0.00 0.174 HD
ATOM 18 HE ARG C 155 8.701 -3.515 2.207 1.00 0.00 0.178 HD
ENDBRANCH 9 10
ENDBRANCH 8 9
ENDBRANCH 7 8
ENDBRANCH 6 7
END_RES ARG C 155
BEGIN_RES LYS C 173
REMARK 5 active torsions:
REMARK status: ('A' for Active; 'I' for Inactive)
REMARK 7 A between atoms: CA and CB
REMARK 8 A between atoms: CB and CG
REMARK 9 A between atoms: CG and CD
REMARK 10 A between atoms: CD and CE
REMARK 11 A between atoms: CE and NZ
ROOT
ATOM 19 CA LYS C 173 20.219 4.162 -5.302 1.00 50.00 0.159 C
ENDROOT
BRANCH 19 20
ATOM 20 CB LYS C 173 19.755 3.421 -4.015 1.00 50.00 0.032 C
BRANCH 20 21
ATOM 21 CG LYS C 173 19.324 4.381 -2.868 1.00 50.00 0.004 C
BRANCH 21 22
ATOM 22 CD LYS C 173 17.980 5.096 -3.175 1.00 50.00 0.032 C
BRANCH 22 23
ATOM 23 CE LYS C 173 17.167 5.409 -1.891 1.00 50.00 0.206 C
BRANCH 23 24
ATOM 24 NZ LYS C 173 15.717 5.449 -2.190 1.00 50.00 -0.064 N
ATOM 25 HZ1 LYS C 173 15.241 6.315 -1.751 1.00 0.00 0.275 HD
ATOM 26 HZ2 LYS C 173 15.530 5.501 -3.253 1.00 0.00 0.275 HD
ATOM 27 HZ3 LYS C 173 15.194 4.583 -1.811 1.00 0.00 0.275 HD
ENDBRANCH 23 24
ENDBRANCH 22 23
ENDBRANCH 21 22
ENDBRANCH 20 21
ENDBRANCH 19 20
END_RES LYS C 173
BEGIN_RES GLU C 245
REMARK 3 active torsions:
REMARK status: ('A' for Active; 'I' for Inactive)
REMARK 12 A between atoms: CB and CG
REMARK 13 A between atoms: CA and CB
REMARK 14 A between atoms: CG and CD
ROOT
ATOM 28 CA GLU C 245 15.647 -0.216 1.861 1.00 50.00 0.160 C
ENDROOT
BRANCH 28 29
ATOM 29 CB GLU C 245 16.271 0.611 0.701 1.00 50.00 0.043 C
BRANCH 29 30
ATOM 30 CG GLU C 245 15.398 1.793 0.201 1.00 50.00 0.100 C
BRANCH 30 31
ATOM 31 CD GLU C 245 15.619 2.074 -1.265 1.00 50.00 0.185 C
ATOM 32 OE2 GLU C 245 16.779 1.915 -1.730 1.00 50.00 -0.647 OA
ATOM 33 OE1 GLU C 245 14.643 2.459 -1.965 1.00 50.00 -0.647 OA
ENDBRANCH 30 31
ENDBRANCH 29 30
ENDBRANCH 28 29
END_RES GLU C 245
BEGIN_RES ASP C 246
REMARK 2 active torsions:
REMARK status: ('A' for Active; 'I' for Inactive)
REMARK 15 A between atoms: CA and CB
REMARK 16 A between atoms: CB and CG
ROOT
ATOM 34 CA ASP C 246 13.335 -2.893 0.394 1.00 50.00 0.170 C
ENDROOT
BRANCH 34 35
ATOM 35 CB ASP C 246 13.926 -3.079 -1.027 1.00 50.00 0.129 C
BRANCH 35 36
ATOM 36 CG ASP C 246 13.478 -1.989 -1.971 1.00 50.00 0.188 C
ATOM 37 OD2 ASP C 246 12.389 -1.405 -1.729 1.00 50.00 -0.647 OA
ATOM 38 OD1 ASP C 246 14.198 -1.694 -2.964 1.00 50.00 -0.647 OA
ENDBRANCH 35 36
ENDBRANCH 34 35
END_RES ASP C 246
BEGIN_RES ASP C 269
REMARK 2 active torsions:
REMARK status: ('A' for Active; 'I' for Inactive)
REMARK 17 A between atoms: CA and CB
REMARK 18 A between atoms: CB and CG
ROOT
ATOM 39 CA ASP C 269 11.714 4.009 2.261 1.00 50.00 0.170 C
ENDROOT
BRANCH 39 40
ATOM 40 CB ASP C 269 11.482 2.477 2.202 1.00 50.00 0.129 C
BRANCH 40 41
ATOM 41 CG ASP C 269 11.775 1.937 0.827 1.00 50.00 0.188 C
ATOM 42 OD1 ASP C 269 12.007 2.752 -0.108 1.00 50.00 -0.647 OA
ATOM 43 OD2 ASP C 269 11.776 0.688 0.672 1.00 50.00 -0.647 OA
ENDBRANCH 40 41
ENDBRANCH 39 40
END_RES ASP C 269
BEGIN_RES ASN C 454
REMARK 2 active torsions:
REMARK status: ('A' for Active; 'I' for Inactive)
REMARK 19 A between atoms: CB and CG
REMARK 20 A between atoms: CA and CB
REMARK I between atoms: CG and ND2
ROOT
ATOM 44 CA ASN C 454 12.580 10.443 -1.722 1.00 50.00 0.169 C
ENDROOT
BRANCH 44 45
ATOM 45 CB ASN C 454 12.806 9.153 -0.888 1.00 50.00 0.119 C
BRANCH 45 46
ATOM 46 CG ASN C 454 11.536 8.609 -0.274 1.00 50.00 0.230 C
ATOM 47 ND2 ASN C 454 11.573 7.374 0.274 1.00 50.00 -0.369 N
ATOM 48 1HD2 ASN C 454 12.411 6.828 0.262 1.00 0.00 0.159 HD
ATOM 49 2HD2 ASN C 454 10.753 6.989 0.698 1.00 0.00 0.159 HD
ATOM 50 OD1 ASN C 454 10.518 9.283 -0.280 1.00 50.00 -0.273 OA
ENDBRANCH 45 46
ENDBRANCH 44 45
END_RES ASN C 454
ENDMDL


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