[Chimera-users] problem of sleap for solvation

[Eric Pettersen]

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 at uab.es
>
>
>
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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