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




_______________________________________________
Chimera-users mailing list
Chimera-users@cgl.ucsf.edu
http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users