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<div class=Section1>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Hi Eric,<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Sorry about that but this still not work. Here are the infos:<o:p></o:p></span></p>
<p class=MsoListParagraph style='text-indent:-18.0pt;mso-list:l1 level1 lfo2'><![if !supportLists]><span
style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><span
style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Os = Windows<o:p></o:p></span></p>
<p class=MsoListParagraph style='text-indent:-18.0pt;mso-list:l1 level1 lfo2'><![if !supportLists]><span
style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><span
style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Built = 15/10/2008<o:p></o:p></span></p>
<p class=MsoListParagraph style='text-indent:-18.0pt;mso-list:l1 level1 lfo2'><![if !supportLists]><span
style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><span
style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Reply log and error message following:<o:p></o:p></span></p>
<p class=MsoListParagraph><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoListParagraph><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Opening 1gcn<o:p></o:p></span></p>
<p class=MsoListParagraph><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Done opening 1gcn<o:p></o:p></span></p>
<p class=MsoListParagraph><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Terminii for #0 determined from SEQRES records<o:p></o:p></span></p>
<p class=MsoListParagraph><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Chain-initial residues that are actual N terminii: HIS 1.A<o:p></o:p></span></p>
<p class=MsoListParagraph><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Chain-initial residues that are not actual N terminii: <o:p></o:p></span></p>
<p class=MsoListParagraph><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Chain-final residues that are actual C terminii: THR 29.A<o:p></o:p></span></p>
<p class=MsoListParagraph><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Chain-final residues that are not actual C terminii: <o:p></o:p></span></p>
<p class=MsoListParagraph><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>15 hydrogen bonds<o:p></o:p></span></p>
<p class=MsoListParagraph><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Hydrogens added<o:p></o:p></span></p>
<p class=MsoListParagraph><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>tempDir: d:\docume~1\jean\config~1\temp\tmpgco3r1<o:p></o:p></span></p>
<p class=MsoListParagraph><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>command: ['C:\\Archivos de programa\\Chimera\\bin\\amber10\\exe\\sleap',
'-f', 'd:\\docume~1\\jean\\config~1\\temp\\tmpgco3r1\\solvate.cmd']<o:p></o:p></span></p>
<p class=MsoListParagraph><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Running sleap command: C:\Archivos de
programa\Chimera\bin\amber10\exe\sleap -f
d:\docume~1\jean\config~1\temp\tmpgco3r1\solvate.cmd<o:p></o:p></span></p>
<p class=MsoListParagraph><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>(solvate) [gtkleap]$ source leaprc.ff03<o:p></o:p></span></p>
<p class=MsoListParagraph><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>(solvate) Error: can not find file leaprc.ff03 in all the search
path.<o:p></o:p></span></p>
<p class=MsoListParagraph><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Failure running sleap <o:p></o:p></span></p>
<p class=MsoListParagraph><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Check reply log for details<o:p></o:p></span></p>
<p class=MsoListParagraph><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoListParagraph><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>All the best,<o:p></o:p></span></p>
<p class=MsoListParagraph><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>JD<o:p></o:p></span></p>
<p class=MsoListParagraph><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<div>
<div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm'>
<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>De:</span></b><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> Eric Pettersen
[mailto:pett@cgl.ucsf.edu] <br>
<b>Enviado el:</b> jueves, 16 de octubre de 2008 20:10<br>
<b>Para:</b> "Dr. Jean-Didier Maréchal"<br>
<b>CC:</b> chimera-dev@cgl.ucsf.edu<br>
<b>Asunto:</b> Re: [chimera-dev] Problem with sleap II<o:p></o:p></span></p>
</div>
</div>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Hi JD,<o:p></o:p></p>
<div>
<p class=MsoNormal><span class=apple-tab-span> </span>I am able to
solvate PDB 1GCN with a 4 angstrom box using last night's build without error.
Can you try the same thing and see if that much works for you? If
not, try again with last night's build. If last night's build works for
1GCN but not your structure, you may have to send me your structure for
debugging purposes. Anyway, let me know what happens.<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal>--Eric<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
<div>
<div>
<p style='margin:0cm;margin-bottom:.0001pt'><span class=apple-converted-space><span
style='font-family:"Helvetica","sans-serif";color:black'>
</span></span><span
style='font-family:"Helvetica","sans-serif";color:black'>Eric Pettersen<o:p></o:p></span></p>
<p style='margin:0cm;margin-bottom:.0001pt'><span class=apple-converted-space><span
style='font-family:"Helvetica","sans-serif";color:black'>
</span></span><span
style='font-family:"Helvetica","sans-serif";color:black'>UCSF Computer Graphics
Lab<o:p></o:p></span></p>
<p style='margin:0cm;margin-bottom:.0001pt'><span class=apple-converted-space><span
style='font-family:"Helvetica","sans-serif";color:black'>
</span></span><span style='font-family:"Helvetica","sans-serif";
color:black'><a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a><o:p></o:p></span></p>
<p class=MsoNormal><span style='font-family:"Helvetica","sans-serif";
color:black'><o:p> </o:p></span></p>
</div>
</div>
<p class=MsoNormal><o:p> </o:p></p>
<div>
<div>
<p class=MsoNormal>On Oct 16, 2008, at 2:59 AM, Dr. Jean-Didier Maréchal wrote:<o:p></o:p></p>
</div>
<p class=MsoNormal><br>
<br>
<o:p></o:p></p>
<div>
<div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:black'>Hi guys,<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:black'> <o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:black'>I could test again the solvation script. As you said, the problem
with the cygwin library is completely solved.<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:black'>I am now running with the following problem:<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:black'> <o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:black'>Running sleap command: C:\Archivos de
programa\Chimera\bin\amber10\exe\sleap -f
d:\docume~1\jean\config~1\temp\tmpfqkue6\solvate.cmd<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:black'>(solvate) [gtkleap]$ source leaprc.ff03<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:black'>(solvate) Error: can not find file leaprc.ff03 in all the search
path.<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:black'>Failure running sleap<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:black'>Check reply log for details<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:black'> <o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:black'>Thanks for any help,<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:black'>JD<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:black'>***************************************************<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:black'>Dr. Jean-Didier Maréchal<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:black'>Lecturer<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:black'>Computational Bioorganic and Bioionorganic Chemistry @ Transmet<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:black'>Unitat de Química Física<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:black'>Departament de Química<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:black'>Universitat Autònoma de Barcelona<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:black'>Edifici C.n.<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:black'>08193 Cerdanyola (Barcelona)<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:black'>Tel: +34.935814936<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:black'>e-mail:<span class=apple-converted-space> </span><a
href="mailto:JeanDidier.Marechal@uab.es">JeanDidier.Marechal@uab.es</a><o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:black'> <o:p></o:p></span></p>
</div>
</div>
<p class=MsoNormal><span style='font-family:"Helvetica","sans-serif";
color:black'>_______________________________________________<br>
Chimera-dev mailing list<br>
<a href="mailto:Chimera-dev@cgl.ucsf.edu">Chimera-dev@cgl.ucsf.edu</a><br>
<a href="http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev">http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev</a><o:p></o:p></span></p>
</div>
</div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
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