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AutoDock, AutoLigand, MGLTools, Vina, PyRx and more.
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PostPosted: Thu Jul 11, 2013 11:23 pm 
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Joined: Thu Jul 11, 2013 11:13 pm
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Hi,

I am sorry if my question sounds like it is due to lack of attention. I have been working with Spartan and it seems to me that it has been installed wrong on the station I am using. I contacted the IT, but.......!! So I am looking for an alternative and time is tight.

My question is:

Can I use autodock for organic molecules?
Based on the description of the program, it seems like yes, but I am not sure.
I will have to determine the torsion angles and the distance between different atoms and the centers of the molecules I made.

Please, please help me.

Thank you,
Sal


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PostPosted: Tue Jul 16, 2013 2:42 am 
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Joined: Fri Sep 21, 2012 3:25 am
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Nope, I think that you want software to draw and validate organic molecules. Am I wrong?
If I am right, I recommend Avogrado, it is free.

Sal wrote:
Hi,

I am sorry if my question sounds like it is due to lack of attention. I have been working with Spartan and it seems to me that it has been installed wrong on the station I am using. I contacted the IT, but.......!! So I am looking for an alternative and time is tight.

My question is:

Can I use autodock for organic molecules?
Based on the description of the program, it seems like yes, but I am not sure.
I will have to determine the torsion angles and the distance between different atoms and the centers of the molecules I made.

Please, please help me.

Thank you,
Sal


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PostPosted: Sat Jan 31, 2015 4:58 am 
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Joined: Sat Jan 31, 2015 4:53 am
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Molecular recognition is a central phenomenon in biology, for example, with enzymes and their substrates, receptors and their signal in ducing ligands, antibodi es and antigens, among others. Given two molecules with 3D conformation s in atomic detail, it is important to know if the molecules bind to each other and, if it is so, what does the formed complex look like (“docking”) and how strong is the binding affinity (that can be related to the “scoring”functions).

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