[Chimera-users] Gasteiger charge
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 Pettersen
> UCSF Computer Graphics Lab
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