[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
>
>
>
> ------------------------------------------------------------------------
>
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> phenixbb at phenix-online.org
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>
--
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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