Hi JD, 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 . --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Oct 9, 2008, at 12:32 AM, Dr. Jean-Didier Maréchal wrote:

Hi Eric,

I followed your instructions. I cleaned my previous chimera, installed 08/10/2008 build, fetch for 1gcn, went to ToolsàAmberàsolvate. Asked from 4ang box, with TIP3PBOX. The hydrogens have therefore been built but then it came with the same message:

Terminii for #0 determined from SEQRES records Chain-initial residues that are actual N terminii: HIS 1.A Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: THR 29.A Chain-final residues that are not actual C terminii: 15 hydrogen bonds Hydrogens added

tempDir: d:\docume~1\jean\config~1\temp\tmpesjllr command: ['C:\\Archivos de programa\\Chimera\\bin\\amber10\\exe\ \sleap', '-f', 'd:\\docume~1\\jean\\config~1\\temp\\tmpesjllr\ \solvate.cmd'] Running sleap command: C:\Archivos de programa\Chimera\bin \amber10\exe\sleap -f d:\docume~1\jean\config~1\temp\tmpesjllr \solvate.cmd Failure running sleap Check reply log for details

Best, JD

De: Eric Pettersen [mailto:pett@cgl.ucsf.edu] Enviado el: jueves, 09 de octubre de 2008 2:57 Para: "Dr. Jean-Didier Maréchal" CC: chimera-users@cgl.ucsf.edu Asunto: Re: [Chimera-users] problem of sleap for solvation

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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