Francis

Any formal charge is written in th PDB file in columns 79-80 as per the PDB format. Running

elbow.builder --smiles "[OH3+]"

results in a PDB file

REMARK 99 electronic Ligand Builder and Optimisation Workbench (eLBOW)
REMARK 99   - a module of PHENIX version 1.3b (Mon Aug 22 04:38:00 2007)
REMARK 99   - file written: Thu Sep 13 09:44:48 2007
REMARK 99
REMARK 99   SMILES string: [OH3+]
ATOM      1 O01 LIG A   1      -0.000   0.000 -0.000 1.00 20.00      A    O 1
ATOM      2 1H01 LIG A   1       1.080   0.000 -0.000 1.00 20.00      A    H 0
ATOM      3 2H01 LIG A   1      -0.540   0.000   0.935 1.00 20.00      A    H 0
ATOM      4 3H01 LIG A   1      -0.540 -0.000 -0.935 1.00 20.00      A    H 0
CONECT    1    2    3    4
CONECT    2    1
CONECT    3    1
CONECT    4    1
END

Plans are afoot to optionally calculate partial charges and put them in the file.

Nigel

On 9/12/2007 11:57 AM, Francis E Reyes wrote:

Ok, this is probably an unsupported feature(TM),but is there anyway to hack elbow.builder to output an electronic charge (presumably from the AM1 calculation) for each atom of a ligand? (by say substituting in for the Bfactor))

Thanks

FR

---------------------------------------------

Francis Reyes M.Sc.

215 UCB

University of Colorado at Boulder

gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D

8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
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Nigel W. Moriarty
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