[Dock-fans] help request about making mol2 files for dock

Trent E. Balius tbalius at aol.com
Thu Apr 12 04:23:42 PDT 2012


Hi Gaurav,




The problem is that the mol file is small, by which I mean that the all the bonds are smaller than the ideal bond length.  Geometry is important for AM1-BCC calculation

I assigned Gasteiger charges and minimized the structure with Amber and obtained a minimized structure where the molecule almost doubled in size.  However, the minimizer messed up some of the angles.

I then used the minimized structure and was able to apply am1-bcc charges in chimera.

I think that scaling the molecule using a transformation matrix may be advisable so that the internal geometry is not changed as happened with minimization.     

Where did you get these MOL files from?  You may consider  converting MOL to Smiles strings and then make the molecules from Simile strings in chimera.     

Find molecules attached. 

I hope this helps,

 

Trent E. Balius
Graduate Student, Rizzo Group
Department of Applied Mathematics and Statistics,
Stony Brook University.
Office: Math Tower 3-129, Phone: (631) 632-8519
URL: http://www.ams.sunysb.edu/~tbalius/

 

 
 
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