I appreciate all your helps!
Thanks!
Fengyun
Quoting Dean Cuebas <deancuebas.missouristate.edu>:
> 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
>>
>>
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>
>
>
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Received on Sat Nov 26 2011 - 15:00:02 PST
