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nguyen
PostPosted: Mon Dec 05, 2011 5:11 am 
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Dear everyone,

I am a new learner. I draw some structures by ChemDraw in 2D and 3D. I used Open Babel to convert but I coudn't the structures by opening Accelrys DS Visualizer.
I also tried with PROGDR and I received many files so I don't know which one is the most suitable for docking?.

Could you give me soma suggestions about that? Also, could you let me know to convert file *.cdx into file.pbd?

Many thanks for your help.


Best wishes,
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kellie
PostPosted: Sat Feb 25, 2012 4:03 am 
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It seems like this free demo at
http://www.molecular-networks.com/node/86
would work. (I am sure that you have already found an answer by now)
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nguyen
PostPosted: Sat Feb 25, 2012 9:36 am 
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Many thanks for your help.
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stefano
PostPosted: Fri Mar 02, 2012 1:55 am 
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Hi,

also OpenBabel supports ChemDraw CDX format, and is free.

Stefano
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cassey04
PostPosted: Sat May 05, 2012 9:07 am 
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Good day, my problem is that while I can look at, say PDB, files from the silicon graphics using Chem3D, I am having trouble viewing Chem3D files. Has someone encountered something alike?
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nguyen
PostPosted: Tue May 08, 2012 2:29 am 
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Hi,

I also have the same problem like you have.

I would like to thank for some answers of yours, however when I access the website to convert, it doesn't have any result. Could you check again for me about this?

About Open Babel software, I tried, however, if we don't select option "Generate 3D", we can not have the file .pdb with viewing the picture of structure as well. The problem here is there are many options for adding hydrogen for ligands, so at the moment, I still don't know which one is the best to use for ligands before docking? This lead to have some errors for ligands if we continues using Autodock Tools to generate file .pdb into file .pdbqt for docking?

Could you give me some suggestions about that?

Many thanks for your help and your time.
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nguyen
PostPosted: Tue May 08, 2012 2:31 am 
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Hi,

I also have the same problem like you have.

I would like to thank for some answers of yours, however when I access the website to convert, it doesn't have any result. Could you check again for me about this?

About Open Babel software, I tried, however, if we don't select option "Generate 3D", we can not have the file .pdb with viewing the picture of structure as well. The problem here is there are many options for adding hydrogen for ligands, so at the moment, I still don't know which one is the best to use for ligands before docking? This lead to have some errors for ligands if we continues using Autodock Tools to generate file .pdb into file .pdbqt for docking?

Could you give me some suggestions about that?

Many thanks for your help and your time.
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dar2133576
PostPosted: Mon May 28, 2012 8:36 pm 
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nguyen wrote:
Hi,

I also have the same problem like you have.

I would like to thank for some answers of yours, however when I access the website to convert, it doesn't have any result. Could you check again for me about this?

About Open Babel software, I tried, however, if we don't select option "Generate 3D", we can not have the file .pdb with viewing the picture of structure as well. The problem here is there are many options for adding hydrogen for ligands, so at the moment, I still don't know which one is the best to use for ligands before docking? This lead to have some errors for ligands if we continues using Autodock Tools to generate file .pdb into file .pdbqt for docking?

Could you give me some suggestions about that?

Many thanks for your help and your time.
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I tried using neuropeptides for ligands but that didn't work either so I'm curious what I should be using to get the best results. If anyone can jump in and make some suggestions that would be great!
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