Dear Fengyun,
Dr. Case is correct. The pKa's for dialkyl triphosphates are all under 1.
Therefore, at anything near physiologic pH, each phosphate=-1, and the
methyl guanosine is +1, leaving you with -2 charge.
Dean
On 11/25/11 11:14 AM, "case" <case.biomaps.rutgers.edu> wrote:
>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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Nov 26 2011 - 14:30:03 PST
