<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi JD,<div><span class="Apple-tab-span" style="white-space:pre"> </span>I am now able to reproduce your problem. It should be fixed in the next daily build. You can fix it in your build directly by copying C:\Archivos de programa\Chimera\inst\cygwin1.dll into C:\Archivos de programa\Chimera\bin\amber10\exe .</div><div><br></div><div>--Eric</div><div><br><div apple-content-edited="true"> <span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>Eric Pettersen</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>UCSF Computer Graphics Lab</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> </span><a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></p><br class="Apple-interchange-newline"></div></span> </div><br><div><div>On Oct 9, 2008, at 12:32 AM, Dr. Jean-Didier Maréchal wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; "><div lang="ES" link="blue" vlink="purple" style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div class="Section1"><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Hi Eric,<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "><o:p> </o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">I followed your instructions. I cleaned my previous chimera, installed 08/10/2008 build, fetch for 1gcn, went to Tools</span><span style="font-size: 11pt; font-family: Wingdings; color: rgb(31, 73, 125); ">à</span><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Amber</span><span style="font-size: 11pt; font-family: Wingdings; color: rgb(31, 73, 125); ">à</span><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">solvate. Asked from 4ang box, with TIP3PBOX. The hydrogens have therefore been built but then it came with the same message:<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "><o:p> </o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Terminii for #0 determined from SEQRES records<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Chain-initial residues that are actual N terminii: HIS 1.A<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Chain-initial residues that are not actual N terminii:<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Chain-final residues that are actual C terminii: THR 29.A<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Chain-final residues that are not actual C terminii:<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">15 hydrogen bonds<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Hydrogens added<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "><o:p> </o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">tempDir: d:\docume~1\jean\config~1\temp\tmpesjllr<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">command: ['C:\\Archivos de programa\\Chimera\\bin\\amber10\\exe\\sleap', '-f', 'd:\\docume~1\\jean\\config~1\\temp\\tmpesjllr\\solvate.cmd']<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Running sleap command: C:\Archivos de programa\Chimera\bin\amber10\exe\sleap -f d:\docume~1\jean\config~1\temp\tmpesjllr\solvate.cmd<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Failure running sleap<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Check reply log for details<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "><o:p> </o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Best,<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">JD<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "><o:p> </o:p></span></div><div><div style="border-right-style: none; border-bottom-style: none; border-left-style: none; border-width: initial; border-color: initial; border-top-style: solid; border-top-color: rgb(181, 196, 223); border-top-width: 1pt; padding-top: 3pt; padding-right: 0cm; padding-bottom: 0cm; padding-left: 0cm; "><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><b><span style="font-size: 10pt; font-family: Tahoma, sans-serif; ">De:</span></b><span style="font-size: 10pt; font-family: Tahoma, sans-serif; "><span class="Apple-converted-space"> </span>Eric Pettersen [<a href="mailto:pett@cgl.ucsf.edu" style="color: blue; text-decoration: underline; ">mailto:pett@cgl.ucsf.edu</a>]<span class="Apple-converted-space"> </span><br><b>Enviado el:</b><span class="Apple-converted-space"> </span>jueves, 09 de octubre de 2008 2:57<br><b>Para:</b><span class="Apple-converted-space"> </span>"Dr. Jean-Didier Maréchal"<br><b>CC:</b><span class="Apple-converted-space"> </span><a href="mailto:chimera-users@cgl.ucsf.edu" style="color: blue; text-decoration: underline; ">chimera-users@cgl.ucsf.edu</a><br><b>Asunto:</b><span class="Apple-converted-space"> </span>Re: [Chimera-users] problem of sleap for solvation<o:p></o:p></span></div></div></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; ">Hi JD,<o:p></o:p></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span class="apple-tab-span"> <span class="Apple-converted-space"> </span></span>I tested solvating 1gcn with the Windows daily build and it worked fine. You shouldn't need to install all those things you tried. You have to realize that when Chimera runs sleap that various environment variables are set that will cause sleap to find files that it won't find it you run it standalone without those environment variables set.<o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span class="apple-tab-span"> <span class="Apple-converted-space"> </span></span>Can you try installing a "clean" version of the daily build and see if you can solvate 1gcn (4 angstrom box) without error? If you get an error, save the contents of the reply log and mail it to me. If you don't get an error then try your structure. If that fails, you will have to send it to me if I'm going to have a chance to debug the problem...<o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; ">--Eric<o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div><div><div><div style="margin-top: 0cm; margin-bottom: 0.0001pt; margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><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></div><div style="margin-top: 0cm; margin-bottom: 0.0001pt; margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><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></div><div style="margin-top: 0cm; margin-bottom: 0.0001pt; margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><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" style="color: blue; text-decoration: underline; ">http://www.cgl.ucsf.edu</a><o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-family: Helvetica, sans-serif; color: black; "><o:p> </o:p></span></div></div></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div><div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; ">On Oct 8, 2008, at 7:12 AM, Dr. Jean-Didier Maréchal wrote:<o:p></o:p></div></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><br><br><o:p></o:p></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><br>Dear all,<br><br>I tried yesterday's build on windows and tested the solvation plugin.<span class="Apple-converted-space"> </span><br>I had a first crash that reply log message I give here:<br><br><span class="apple-tab-span"> <span class="Apple-converted-space"> </span></span>command: ['C:\\Archivos de<br>programa\\Chimera\\bin\\amber10\\exe\\sleap', '-f',<br>'d:\\docume~1\\jean\\config~1\\temp\\tmp7wpvvm\\solvate.cmd']<br><span class="apple-tab-span"> <span class="Apple-converted-space"> </span></span>Running sleap command: C:\Archivos de<br>programa\Chimera\bin\amber10\exe\sleap -f<br>d:\docume~1\jean\config~1\temp\tmp7wpvvm\solvate.cmd<br><span class="apple-tab-span"> <span class="Apple-converted-space"> </span></span>Failure running sleap<span class="Apple-converted-space"> </span><br><span class="apple-tab-span"> <span class="Apple-converted-space"> </span></span>Check reply log for details<br><br>Running C:\Archivos de programa\Chimera\bin\amber10\exe\sleap alone, I saw<br>that cygwin1.dll was missing. So I installed it in the same directory.<span class="Apple-converted-space"> </span><br><br>Then came a second crash:<br><br><span class="apple-tab-span"> <span class="Apple-converted-space"> </span></span>tempDir: d:\docume~1\jean\config~1\temp\tmp6m0sm0<br><span class="apple-tab-span"> <span class="Apple-converted-space"> </span></span>command: ['C:\\Archivos de<br>programa\\Chimera\\bin\\amber10\\exe\\sleap', '-f',<br>'d:\\docume~1\\jean\\config~1\\temp\\tmp6m0sm0\\solvate.cmd']<br><span class="apple-tab-span"> <span class="Apple-converted-space"> </span></span>Running sleap command: C:\Archivos de<br>programa\Chimera\bin\amber10\exe\sleap -f<br>d:\docume~1\jean\config~1\temp\tmp6m0sm0\solvate.cmd<br><span class="apple-tab-span"> <span class="Apple-converted-space"> </span></span>(solvate) [gtkleap]$ source leaprc.ff03<br><span class="apple-tab-span"> <span class="Apple-converted-space"> </span></span>(solvate) Error: can not find file leaprc.ff03 in all the search<br>path.<br><span class="apple-tab-span"> <span class="Apple-converted-space"> </span></span>Failure running sleap<span class="Apple-converted-space"> </span><br><span class="apple-tab-span"> <span class="Apple-converted-space"> </span></span>Check reply log for details<br><br>Though I located the leaprc.ff03 file in another directory and copied it in<br>the running one, I can not pass over this problem.<br><br>All the best!<span class="Apple-converted-space"> </span><br><br>JD<br><br><br>***************************************************<br>Dr. Jean-Didier Maréchal<br>Lecturer<br>Computational Bioorganic and Bioionorganic Chemistry @ Transmet<br>Unitat de Química Física<br>Departament de Química<br>Universitat Autònoma de Barcelona<br>Edifici C.n.<br>08193 Cerdanyola (Barcelona)<br>Tel: +34.935814936<br>e-mail:<span class="Apple-converted-space"> </span><a href="mailto:JeanDidier.Marechal@uab.es" style="color: blue; text-decoration: underline; ">JeanDidier.Marechal@uab.es</a><br><br><br><br><br>_______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu" style="color: blue; text-decoration: underline; ">Chimera-users@cgl.ucsf.edu</a><br><a href="http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users" style="color: blue; text-decoration: underline; ">http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><o:p></o:p></div></div></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div></div></div></div></span></blockquote></div><br></div></body></html>