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@uab.es
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@uab.es
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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@cgl.ucsf.edu] Enviado el: jueves, 16 de octubre de 2008 20:10 Para: "Dr. Jean-Didier Maréchal" CC: chimera-dev@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@uab.es _______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev
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Dr. Jean-Didier Maréchal -
Eric Pettersen