[phenixbb] elbow.builder to generate charges on individual atoms?

Nigel W. Moriarty nwmoriarty at lbl.gov
Thu Sep 13 09:48:15 PDT 2007


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
>
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb
>   

-- 
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709
Fax   : 510-486-5909
Email : NWMoriarty at LBL.gov
Web   : CCI.LBL.gov

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