Hi JD, 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. 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... --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Oct 8, 2008, at 7:12 AM, Dr. Jean-Didier Maréchal wrote:
Dear all,
I tried yesterday's build on windows and tested the solvation plugin. I had a first crash that reply log message I give here:
command: ['C:\\Archivos de programa\\Chimera\\bin\\amber10\\exe\\sleap', '-f', 'd:\\docume~1\\jean\\config~1\\temp\\tmp7wpvvm\\solvate.cmd'] Running sleap command: C:\Archivos de programa\Chimera\bin\amber10\exe\sleap -f d:\docume~1\jean\config~1\temp\tmp7wpvvm\solvate.cmd Failure running sleap Check reply log for details
Running C:\Archivos de programa\Chimera\bin\amber10\exe\sleap alone, I saw that cygwin1.dll was missing. So I installed it in the same directory.
Then came a second crash:
tempDir: d:\docume~1\jean\config~1\temp\tmp6m0sm0 command: ['C:\\Archivos de programa\\Chimera\\bin\\amber10\\exe\\sleap', '-f', 'd:\\docume~1\\jean\\config~1\\temp\\tmp6m0sm0\\solvate.cmd'] Running sleap command: C:\Archivos de programa\Chimera\bin\amber10\exe\sleap -f d:\docume~1\jean\config~1\temp\tmp6m0sm0\solvate.cmd (solvate) [gtkleap]$ source leaprc.ff03 (solvate) Error: can not find file leaprc.ff03 in all the search path. Failure running sleap Check reply log for details
Though I located the leaprc.ff03 file in another directory and copied it in the running one, I can not pass over this problem.
All the best!
JD
*************************************************** Dr. Jean-Didier Maréchal Lecturer Computational Bioorganic and Bioionorganic Chemistry @ Transmet Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal@uab.es
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