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 Post subject: pdbqt
PostPosted: Wed Jan 22, 2014 9:48 am 
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Millimolar User
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Joined: Wed Jan 22, 2014 9:39 am
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Hi all,
I am using autodock vina .I have produce some other small molecular, but I can't produce the pdbqt file of CH3CN .I don't know why. Who can help me ?


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 Post subject: Re: pdbqt
PostPosted: Wed Feb 12, 2014 6:23 pm 
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You could use openbabel for this (it is included in he latest version of MGLToolsPckgs)

Here's how:
1. create a file 'ccn.smi' containing "CCN"
2. determine the path to your local copy of obabel
3. create result.pdbqt:
path_to_local_obabel/obabel -ismi ccn.smi -opdbqt -p 7 --gen3D > result.pdbqt

Here is my result.pdbqt (note the 3D coordinates will vary slightly):

REMARK Name =
REMARK x y z vdW Elec q Type
REMARK _______ _______ _______ _____ _____ ______ ____
ROOT
ATOM 1 N LIG 1 3.051 1.116 0.655 0.00 0.00 -0.330 NA
ATOM 2 H LIG 1 4.069 1.131 0.616 0.00 0.00 +0.118 HD
ATOM 3 H LIG 1 2.734 1.959 0.178 0.00 0.00 +0.118 HD
ENDROOT
BRANCH 1 5
ATOM 4 C LIG 1 1.038 -0.071 -0.056 0.00 0.00 +0.020 C
ATOM 5 C LIG 1 2.557 -0.061 -0.047 0.00 0.00 +0.074 C
ENDBRANCH 1 5
TORSDOF 1


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