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PostPosted: Wed Nov 27, 2013 8:11 am 
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Hi all, I am using vina, and recently tested residue flexibility. It worked perfectly but how I can recover the residue conformation corresponding to given docking poses?
Thank you for your help
Pierre


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PostPosted: Mon Dec 02, 2013 7:30 pm 
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When flexible residues are included in a vina calculation, their docked poses are included in each "MODEL" in the output pdbqt file after all the ligand atoms (and can be visualized in ADT). Here's part of an example result:

MODEL 1
REMARK VINA RESULT: -11.3 0.000 0.000
REMARK 14 active torsions:
REMARK status: ('A' for Active; 'I' for Inactive)
REMARK 1 A between atoms: N1_1 and C31_39
REMARK 2 A between atoms: C2_3 and C3_4
REMARK I between atoms: C3_4 and N2_6
REMARK 3 A between atoms: N2_6 and C4_7
REMARK 4 A between atoms: N3_11 and C10_14
REMARK 5 A between atoms: C10_14 and C11_15
REMARK 6 A between atoms: C11_15 and O2_16
REMARK 7 A between atoms: C11_15 and C12_17
REMARK 8 A between atoms: C12_17 and C13_18
REMARK 9 A between atoms: C13_18 and C14_19
REMARK 10 A between atoms: C13_18 and C21_26
REMARK 11 A between atoms: C14_19 and C15_20
REMARK I between atoms: C21_26 and N4_28
REMARK 12 A between atoms: N4_28 and C22_29
REMARK 13 A between atoms: C23_30 and O4_31
REMARK 14 A between atoms: C31_39 and C32_40
ROOT
HETATM 1 C11 IND I 201 2.437 4.306 -7.693 1.00 21.68 0.136 C
ENDROOT
BRANCH 1 2
HETATM 2 C10 IND I 201 2.367 4.129 -6.176 1.00 20.86 0.149 C
BRANCH 2 3
HETATM 3 N3 IND I 201 2.707 5.318 -5.423 1.00 28.91 -0.395 N
HETATM 4 C8 IND I 201 4.153 5.286 -5.091 1.00 26.24 0.148 C
HETATM 5 C9 IND I 201 4.682 6.355 -4.157 1.00 27.47 0.292 C
HETATM 6 N1 IND I 201 3.818 6.778 -3.147 1.00 28.25 0.096 N
HETATM 7 C1 IND I 201 2.472 6.950 -3.759 1.00 30.30 0.307 C
HETATM 8 C2 IND I 201 1.731 5.782 -4.375 1.00 27.27 0.200 C
BRANCH 6 9
HETATM 9 C31 IND I 201 4.328 7.880 -2.323 1.00 36.25 0.312 C
BRANCH 9 10
HETATM 10 C32 IND I 201 4.155 7.885 -0.800 1.00 42.75 -0.013 A
HETATM 11 C33 IND I 201 3.224 8.699 -0.138 1.00 47.41 0.125 A
HETATM 12 N5 IND I 201 2.994 8.743 1.246 1.00 51.38 -0.273 NA
HETATM 13 C34 IND I 201 3.829 7.850 1.915 1.00 50.60 0.116 A
HETATM 14 C35 IND I 201 4.777 7.012 1.319 1.00 49.34 0.020 A
HETATM 15 C36 IND I 201 4.944 7.028 -0.064 1.00 44.71 0.012 A
ENDBRANCH 9 10
ENDBRANCH 6 9
..............
BEGIN_RES ARG A 8
REMARK 4 active torsions:
REMARK status: ('A' for Active; 'I' for Inactive)
REMARK 1 A between atoms: CA and CB
REMARK 2 A between atoms: CB and CG
REMARK 3 A between atoms: CG and CD
REMARK 4 A between atoms: CD and NE
REMARK I between atoms: NE and CZ
REMARK I between atoms: CZ and NH1
REMARK I between atoms: CZ and NH2
ROOT
ATOM 1 CA ARG A 8 1.594 -2.573 -17.153 1.00 29.87 0.159 C
ENDROOT
BRANCH 1 2
ATOM 2 CB ARG A 8 0.909 -1.217 -17.386 1.00 28.16 0.035 C
BRANCH 2 3
ATOM 3 CG ARG A 8 -0.027 -0.755 -16.268 1.00 27.47 0.039 C
BRANCH 3 4
ATOM 4 CD ARG A 8 0.016 0.782 -16.119 1.00 25.45 0.196 C
BRANCH 4 5
ATOM 5 NE ARG A 8 -1.125 1.429 -16.755 1.00 23.06 -0.279 N
ATOM 6 CZ ARG A 8 -1.085 2.600 -17.392 1.00 28.80 0.341 C
ATOM 7 NH1 ARG A 8 0.058 3.238 -17.574 1.00 30.95 -0.292 N
ATOM 8 NH2 ARG A 8 -2.201 3.145 -17.842 1.00 26.02 -0.292 N
ATOM 9 2HH1 ARG A 8 0.898 2.850 -17.237 0.00 0.00 0.255 HD
ATOM 10 1HH1 ARG A 8 0.071 4.102 -18.047 0.00 0.00 0.255 HD
ATOM 11 2HH2 ARG A 8 -3.061 2.687 -17.706 0.00 0.00 0.255 HD
.........


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PostPosted: Thu Jan 08, 2015 12:02 pm 
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Thanks for sharing with us this type of question.

International Yoga Festival 2015


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