[Chimera-users] problem of sleap for solvation

[Eric Pettersen]

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 at cgl.ucsf.edu]
> Enviado el: jueves, 09 de octubre de 2008 2:57
> Para: "Dr. Jean-Didier Maréchal"
> CC: chimera-users at 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 at uab.es
>
>
>
>
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