[Dock-fans] help request about making mol2 files for dock
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
Institute of Structural and Molecular Biology
Michael Swann Building
University of Edinburgh
Edinburgh, EH9 3JR, UK
Tel. 0131 650 7358
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Scotland, with registration number SC005336.
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