Re: [AMBER] question on antechamber generating parameters for a charged ligand

From: Dean Cuebas <deancuebas.missouristate.edu>
Date: Sat, 26 Nov 2011 16:02:16 -0600

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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Received on Sat Nov 26 2011 - 14:30:03 PST
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