ADL: AMIDE_BOND_rotable

mswingle at jaguar1.usouthal.edu mswingle at jaguar1.usouthal.edu
Mon Oct 22 20:09:49 PDT 2007


Hi Maria,

Are you trying to model main chain cis-trans isomerization? I believe this is beyond the 
capabilities of autodock. You probably need to make separate receptor models for each 
isomer with an application like AMBER (or maybe by homology modeling, if you can find 
appropriate templates) and do separate docking runs.


Regards,

Mark

----- Original Message -----
From: maria giovanna chini <mariagiovchini3 at hotmail.it>
Date: Monday, October 22, 2007 6:45 am
Subject: ADL: AMIDE_BOND_rotable
To: autodock at scripps.edu


> Hi all,
> 
> I am a young user of AutodocK 4.0 with Mgltools 1.4.5 and i am trying 
> to move receptor in my docking; i have prepared receptor for my 
> calculation using both by the python script "prepare_flexreceptor4.py" 
> and by ADT, but amide bond is always NON ROTABLE!!
> How can i render amide bond rotable?????
> 
> Thank  you in advance  
> 
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