[chimera-dev] Problem with sleap II

[Dr. Jean-Didier Maréchal]

Hi Eric,

 

Sorry about that but this still not work. Here are the infos:

1.       Os = Windows

2.       Built = 15/10/2008

3.       Reply log and error message following:

 

Opening 1gcn

Done opening 1gcn

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\tmpgco3r1

command:  ['C:\\Archivos de programa\\Chimera\\bin\\amber10\\exe\\sleap',
'-f', 'd:\\docume~1\\jean\\config~1\\temp\\tmpgco3r1\\solvate.cmd']

Running sleap command: C:\Archivos de programa\Chimera\bin\amber10\exe\sleap
-f d:\docume~1\jean\config~1\temp\tmpgco3r1\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

 

All the best,

JD

 

De: Eric Pettersen [mailto:pett at cgl.ucsf.edu] 
Enviado el: jueves, 16 de octubre de 2008 20:10
Para: "Dr. Jean-Didier Maréchal"
CC: chimera-dev at cgl.ucsf.edu
Asunto: Re: [chimera-dev] Problem with sleap II

 

Hi JD,

            I am able to solvate PDB 1GCN with a 4 angstrom box using last
night's build without error.  Can you try the same thing and see if that
much works for you?  If not, try again with last night's build.  If last
night's build works for 1GCN but not your structure, you may have to send me
your structure for debugging purposes.  Anyway, let me know what happens.

 

--Eric

 

                        Eric Pettersen

                        UCSF Computer Graphics Lab

                        http://www.cgl.ucsf.edu

 

 

On Oct 16, 2008, at 2:59 AM, Dr. Jean-Didier Maréchal wrote:





Hi guys,

 

I could test again the solvation script. As you said, the problem with the
cygwin library is completely solved.

I am now running with the following problem:

 

Running sleap command: C:\Archivos de programa\Chimera\bin\amber10\exe\sleap
-f d:\docume~1\jean\config~1\temp\tmpfqkue6\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

 

Thanks for any help,

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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