ADL: recurrent question: charge assignment

Sargis Dallakyan sargis at scripps.edu
Mon Jan 7 13:17:18 PST 2008


> However, when using Autodock Tools to assign Gasteiger charges to the receptor, it also changes the protonation and tautomer states to its defaults (ie. neutral HIS, negative ASP and GLU, positive LYS and ARG), screewing up any previous work done (out from ADT) to set those. Therefore, is there any way to avoid this? 

Hi Jordi,

Are you using Edit -> Charges -> Compute Gasteiger to assign Gasteiger charges 
to the receptor? If so, it is not supposed to add or remove any atom from the 
molecule. If, on the other hand, you are using Grid -> Macromolecule -> Choose, 
it does remove non-polar hydrogens, by default, but it should not mess up the 
protonation state of the residues you mentioned (ie. neutral HIS, negative ASP 
and GLU, positive LYS and ARG).

I don't quite understand why this did not work in you case, that's why I'd 
recommend to use our Bugzilla http://mgldev.scripps.edu/bugs/ to submit a 
feature request. Please include input files, if any, as an attachment.

Thanks,
Sargis


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