On Mon, Oct 29, 2012, anyiphysics.gmail.com wrote:
>
> I'm now using antechamber to derive partial charges for some large organic
> molecules. My input file is pdb and I want to get mol2 files for these
> molecules. My problem is when the molecule contains more than 150 atoms, I
> can only get the sqm.out file. I can't get the mol2 file even though the
> sqm.out says the geometry is converged. However, if the molecule has <150
> atoms then I don't have this problem.
What happens? Is there any error message? You might post the pdb file with
more than 150 atoms that is giving the error.
Still, Dan and Francois are correct: most molecules at this size can (should?)
be broken into fragments for generation of force field parameters.
...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Nov 01 2012 - 11:00:05 PDT
