[Chimera-users] Gasteiger charge

Ibrahim Moustafa I.moustafa at psu.edu
Thu Oct 13 15:23:09 PDT 2011

Thanks Eric for your reply.  I will wait for the new build.
However, I have other NTP analogue to prepare for docking; so, I still need
to find a way to correctly assign the Gasteiger charges for these ligands.

 I used AddH separately, the program does not add H to the phosphate group.

  Thanks for help,

On 10/13/11 6:11 PM, "Eric Pettersen" <pett at cgl.ucsf.edu> wrote:

> On Oct 13, 2011, at 1:29 PM, Ibrahim Moustafa wrote:
>>   Gasteiger charge
>>  Dear Chimera developers:
>>    I want to assign Gasteiger charges for a ligand, as a preparative step for
>> docking.  The ligand is GTP, extracted from a protein complex structure.
>>    I wanted to add the Gasteiger partial charge, and explicitly chose to have
>> a total charge of ³-4² on the ligand molecule.  However, the program assigned
>> partial charges that sum to total charge of ³-2² instead of ³-4².
>>    Any idea why the program assigned the Gasteiger partial charges
>> incorrectly, ignoring the input total charge on the ligand.
> Amber's antechamber program (which Chimera uses for charge assignment) does
> not honor the '-nc' flag (net charge) for Gasteiger charges.  It just uses
> what it believes the charge to be, which I guess in this case is -2 (weird
> choice!).  You can see complaints about this if you google for "gasteiger"
> along with "nc".
> If you use the latest daily build (tomorrow's!) then you can use AM1-BCC
> charges for GTP.  We've added "charge templates" for GTP/GDP/ADP/ATP since
> antechamber frequently fails with highly negatively-charged systems, so we
> used charges taken from the Amber parameter database
> <http://www.pharmacy.manchester.ac.uk/bryce/amber/>  for those commonplace
> residues.  However, in constructing the template for GTP I missed HO3', so
> that's why you would need to get tomorrow's build.
> Finally, you should probably use AddH separately and see if Chimera adds a
> proton to the terminal phosphate of your GTP.  If it does, delete it before
> adding charges.  The template charges are for GTPs with no protonation on the
> terminal phosphate.
> --Eric
>                         Eric Pettersen
>                         UCSF Computer Graphics Lab
>                         http://www.cgl.ucsf.edu

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