Re: ADL: fixing non-integral charges

["Flight, Robert Maxwell" <l72k6$at$unb.ca>]

Hi Alex,
 > 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
 -0.520
 > ATOM      2  HN1 ALA A 295      76.335  59.392  19.139  1.00  0.00
 0.000
 > ATOM      3  HN2 ALA A 295      76.036  59.070  17.502  1.00  0.00
 0.000
 > ATOM      4  HN3 ALA A 295      77.509  59.124  17.946  1.00  0.00
 0.000
 > ATOM      5  CA  ALA A 295      76.552  57.441  18.657  1.00 15.00
 0.215
 > ATOM      6  C   ALA A 295      76.956  56.616  17.418  1.00 18.88
 0.526
 > ATOM      7  O   ALA A 295      77.711  55.640  17.578  1.00 17.66
 -0.500
 > ATOM      8  CB  ALA A 295      75.172  57.039  19.105  1.00 12.54
 0.031
 > From what you show here, I'm guessing that the alanine is at a break point
 in the
 protein (if it was continuous then the Nitrogen should have only one H like the
 other
 one you listed), you should visually check this to be sure.  I have personally
 had a
 lot of trouble with partial charges on any residues that are at a break in my
 proteins.
 > 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
 or part
 of the active site, and I have not noticed it making any difference in my
 docking
 results.  If you really wanted, you could distribute a positive 0.248 charge
 evenly
 between the three hydrogens.  That would be the safe bet, and is relatively
 painless if
 you only have to do it once.
 Hope this helps.
 Cheers,
 -Robert
 ***************************
 Robert Flight
 Master Candidate
 Computational Chemistry
 Department of Chemistry
 University of New Brunswick
 Fredericton  NB, Canada  E3B 6E2
 e-mail: robert.flight$at$unb.ca
 ***************************
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