On Fri, Nov 25, 2011, fn1.rice.edu wrote:
> antechamber -i GTG-align_h.pdb -fi pdb -o gtg.mol2 -fo mol2 -c bcc -nc -s -2
^^^^^
This is wrong: the "-nc" flag needs an argument, giving the net charge, such
as "-nc -1". Note: antechamber does *not* try to figure out the net charge on
the molecule; rather, the user has to provide that (default is zero).
> >> 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE
My "guess" is that the net charge is -2 (+1 for the methyl-guanosine, -3 for
the three phosphate groups. But check this yourself.
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Nov 25 2011 - 09:30:03 PST
