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Francis<br>
<br>
Any formal charge is written in th PDB file in columns 79-80 as per the
PDB format. Running<br>
<br>
elbow.builder --smiles "[OH3+]"<br>
<br>
results in a PDB file<br>
<br>
REMARK 99 electronic Ligand Builder and Optimisation Workbench (eLBOW)<br>
REMARK 99 - a module of PHENIX version 1.3b (Mon Aug 22 04:38:00
2007)<br>
REMARK 99 - file written: Thu Sep 13 09:44:48 2007<br>
REMARK 99<br>
REMARK 99 SMILES string: [OH3+]<br>
ATOM 1 O01 LIG A 1 -0.000 0.000 -0.000 1.00 20.00
A O 1<br>
ATOM 2 1H01 LIG A 1 1.080 0.000 -0.000 1.00 20.00
A H 0<br>
ATOM 3 2H01 LIG A 1 -0.540 0.000 0.935 1.00 20.00
A H 0<br>
ATOM 4 3H01 LIG A 1 -0.540 -0.000 -0.935 1.00 20.00
A H 0<br>
CONECT 1 2 3 4<br>
CONECT 2 1<br>
CONECT 3 1<br>
CONECT 4 1<br>
END<br>
<br>
Plans are afoot to optionally calculate partial charges and put them in
the file.<br>
<br>
Nigel<br>
<br>
On 9/12/2007 11:57 AM, Francis E Reyes wrote:
<blockquote cite="mid:87DEA551-85FB-4AA3-AF35-4C7F29F6F41B@colorado.edu"
type="cite">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))
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<div>Thanks</div>
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<div>FR</div>
<div><br>
<div> <span class="Apple-style-span"
style="border-collapse: separate; border-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px;">
<div style="margin: 0px;">---------------------------------------------</div>
<div style="margin: 0px;">Francis Reyes M.Sc.</div>
<div style="margin: 0px;">215 UCB</div>
<div style="margin: 0px;">University of Colorado at Boulder</div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal; min-height: 14px;"><br>
</div>
<div style="margin: 0px;">gpg --keyserver pgp.mit.edu --recv-keys
67BA8D5D</div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal; min-height: 14px;"><br>
</div>
<div style="margin: 0px;">8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669
67BA 8D5D</div>
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<br class="Apple-interchange-newline">
</span> </div>
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</blockquote>
<br>
<pre class="moz-signature" cols="72">--
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 : <a class="moz-txt-link-abbreviated" href="mailto:NWMoriarty@LBL.gov">NWMoriarty@LBL.gov</a>
Web : CCI.LBL.gov</pre>
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