ADL: recurrent question: charge assignment

Jordi jbvqob at
Fri Jan 4 12:41:20 PST 2008


Sorry if this is a recurrent question (I know it is...) but I think that many of us are a little confused about what charges should be used with Autodock 4. A few weeks ago, I read a post from G.M. Morris saying that Autodock 4 has been parameterized with Gasteiger charges either for the ligands and for the receptors and that using a different set of charges (ie. AMBER charges,....) is possible but it would require to calculate new parameters in order to achieve a good correlation between calculated and experimental DeltaG of binding. If this is correct (is it?) then it is obvious that Gasteiger's is the right choice if you don't want to do that extra work.
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? I know that ADT has a module that can be used to set the HIS protonation state but still is a pain if one has already done this with some other program and only wants to assign Gasteiger partial charges without changing anything else. I have tried to assign Gasteiger charges with different programs other than ADT but it seems that the results are not the same therefore are we forced to use ADT somehow?

Thanks for any comments or clarifications.


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