[Chimera-users] Gasteiger charge

[Ibrahim Moustafa]

Thanks Elaine for the clarification.

 Ibrahim


On 10/13/11 6:32 PM, "Elaine Meng" <meng at 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.h
> 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 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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>