Re: ADL: fixing non-integral charges
- From: "Flight, Robert Maxwell"
- Subject: Re: ADL: fixing non-integral charges
- Date: Mon, 3 Nov 2003 10:42:33 -0400
> I am trying to use autodock via adt. When I read in my ligand it
> complains that the charge on the molecule is not integral and to fix
> this in the written file and mentions specific residues. From the
> written pdbq file an example is
> ATOM 1 N ALA A 295 76.602 58.846 18.320 1.00 15.64
> ATOM 2 HN1 ALA A 295 76.335 59.392 19.139 1.00 0.00
> ATOM 3 HN2 ALA A 295 76.036 59.070 17.502 1.00 0.00
> ATOM 4 HN3 ALA A 295 77.509 59.124 17.946 1.00 0.00
> ATOM 5 CA ALA A 295 76.552 57.441 18.657 1.00 15.00
> ATOM 6 C ALA A 295 76.956 56.616 17.418 1.00 18.88
> ATOM 7 O ALA A 295 77.711 55.640 17.578 1.00 17.66
> ATOM 8 CB ALA A 295 75.172 57.039 19.105 1.00 12.54
> From what you show here, I'm guessing that the alanine is at a break point
protein (if it was continuous then the Nitrogen should have only one H like the
one you listed), you should visually check this to be sure. I have personally
lot of trouble with partial charges on any residues that are at a break in my
> ie it only has HN not HN1,2,3 and the charge on it is .248 thus giving a
> net charge of 0.
> So to fix this file do I want to simply delete the extra HN lines and
> change the charge from 0 to 0.248 or do I fix it some other way?
Personally, I have started ignoring the message as long as residue was not near
of the active site, and I have not noticed it making any difference in my
results. If you really wanted, you could distribute a positive 0.248 charge
between the three hydrogens. That would be the safe bet, and is relatively
you only have to do it once.
Hope this helps.
Department of Chemistry
University of New Brunswick
Fredericton NB, Canada E3B 6E2
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