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

Douglas Houston dhouston at staffmail.ed.ac.uk
Thu Apr 12 04:30:25 PDT 2012


My guess is that these "small" files were written out by ChemDraw -  
this is a known problem with this software package.


Quoting "Trent E. Balius" <tbalius at aol.com> on Thu, 12 Apr 2012  
07:23:42 -0400 (EDT):

> 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/
>
>
>
>
>
>




_____________________________________________________
Dr. Douglas R. Houston
Lecturer
Room 3.23
Institute of Structural and Molecular Biology
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