ADL: gasteiger charges
demet.akten at gmail.com
Thu May 8 02:17:41 PDT 2008
Thank you for the reply.
I have compared sigma values of PETRA and ADT values, few of them
still do not match.
Would it be caused by merged hydrogens in ADT? I have added non-polar
hydrogens' sigma values to the sigma values of the atoms to which it
is attached, but still I get different results.
On May 7, 2008, at 3:08 PM, Tomek Wlodarski wrote:
> Dear Demet,
> AD calculates only Gasteiger sigma charges (PEOE) - as far as I
> PETRA instead could calculate sigma, pi or total (sum of sigma
> and pi
> charges) Gasteiger charges.
> So if your ligand has pi systems - you would have different
> results in
> PETRA then in AutoDock.
> I hope this is would help you,
> Tomek Wlodarski
> On Wed, May 7, 2008 at 12:59 PM, Demet Akten
> <demet.akten at gmail.com> wrote:
>> Dear all,
>> I have an inhibitor called "2-(p-aminophenyl)-6-
>> sulfonic acid" for which I have calculated Gasteiger charges using
>> ADT. It returned a non-integer charge of -1.5. Then I used PETRA
>> server, the total charge is returned as -1, which is as expected
>> (sulfate group carries one negative charge). When I check the charges
>> assigned to every atom, I see differences which are significant for
>> some atoms, between the results of ADT and PETRA. Do you think there
>> might be a bug in ADT calculations?
>> Thank you,
>> Demet Akten-Akdogan, Ph.D.
>> Research Associate
>> Polymer Research Center
>> Bogazici University
>> email: demet.akten at gmail.com
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