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. Thanks in advance for your help. Regards, Ibrahim -- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., University Park, Pennsylvania State University PA 16802 Tel. (814) 863-8703 Fax (814) 865-7927
On Oct 13, 2011, at 1:29 PM, Ibrahim Moustafa wrote:
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 “-4” on the ligand molecule. However, the program assigned partial charges that sum to total charge of “-2” instead of “-4”.
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 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
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, Ibrahim On 10/13/11 6:11 PM, "Eric Pettersen" <pett@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
Hi Ibrahim, Unfortunately this problem is out of our hands -- it is in Antechamber, which is developed separately. I don't think it will be possible to use Chimera (which uses Antechamber) to get the net charges you want with the Gasteiger calculation. Eric added charge lookup for GTP, GDP, ATP, ADP, taken from the Amber parameter database. http://www.pharmacy.manchester.ac.uk/bryce/amber#cof This database includes other cofactors but not other NTPs. Sorry about that, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco P.S. here is more information at the Amber parm database on how the parameters for GTP,GDP,ATP,ADP were calculated http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/cof/phos_inf... On Oct 13, 2011, at 3:23 PM, Ibrahim Moustafa wrote:
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, Ibrahim
On 10/13/11 6:11 PM, "Eric Pettersen" <pett@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 “-4” on the ligand molecule. However, the program assigned partial charges that sum to total charge of “-2” instead of “-4”.
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
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Thanks Elaine for the clarification. Ibrahim On 10/13/11 6:32 PM, "Elaine Meng" <meng@cgl.ucsf.edu> wrote:
Hi Ibrahim, Unfortunately this problem is out of our hands -- it is in Antechamber, which is developed separately. I don't think it will be possible to use Chimera (which uses Antechamber) to get the net charges you want with the Gasteiger calculation.
Eric added charge lookup for GTP, GDP, ATP, ADP, taken from the Amber parameter database. http://www.pharmacy.manchester.ac.uk/bryce/amber#cof
This database includes other cofactors but not other NTPs. Sorry about that, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
P.S. here is more information at the Amber parm database on how the parameters for GTP,GDP,ATP,ADP were calculated http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/cof/phos_inf... tml
On Oct 13, 2011, at 3:23 PM, Ibrahim Moustafa wrote:
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, Ibrahim
On 10/13/11 6:11 PM, "Eric Pettersen" <pett@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
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Elaine Meng -
Eric Pettersen -
Ibrahim Moustafa