[gmx-users] luck

Mr Bernard Ramos bgrquantum at yahoo.com
Tue Feb 1 19:48:35 CET 2011


thanks. It was able to generate the needed files as indicated in the tutorial. I trnasfered my working directory.
 
many thanks.
 
Bernard

--- On Wed, 2/2/11, Justin A. Lemkul <jalemkul at vt.edu> wrote:


From: Justin A. Lemkul <jalemkul at vt.edu>
Subject: Re: [gmx-users] luck
To: "Gromacs Users' List" <gmx-users at gromacs.org>
Date: Wednesday, February 2, 2011, 2:32 AM




Mr Bernard Ramos wrote:
> 
> this is the command i am using:
>  pbd2gmx -f 1AKI.pdb -o 1AKI_processed.gro -water spce
> then I choose a force fileld.
> then I get the error and no new files generated at all.
>  My working directory is:
> /cygdrive/c/MDProgram/Gromacs453/bin/molecule tests
> 

I assume that .../Gromacs453/bin is the location where the Gromacs binaries are installed?  It's a bad idea to run commands from the location of the installation or its subdirectories.  It's also a possibility that the space in "molecule tests" is causing problems with filename parsing, but that's a bit of a guess.

Move the necessary files to a new location, in a directory named without spaces, and try again.

-Justin

> --- On *Wed, 2/2/11, Justin A. Lemkul /<jalemkul at vt.edu>/* wrote:
> 
> 
>     From: Justin A. Lemkul <jalemkul at vt.edu>
>     Subject: Re: [gmx-users] luck
>     To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>     Date: Wednesday, February 2, 2011, 2:15 AM
> 
> 
> 
>     Mr Bernard Ramos wrote:
>      > Hi!
>      >  I am actually following your lysozyme tutorial. I ve been using
>     different pdb files including that of water, methanol, 1AKI, etc.
>     The pdb2gmx does not generate any topology file. No files are
>     generated and I get this error:
>      >  ------------------------------------------
>      > pdb2gmx, VERSION 4.5.3
>      > Source code file: futil.c, line:491
>      >  File input/output
>      > 1AKI.pdb
>      > For more.... etc
>      > ------------------------------------------
>      >
> 
>     Then this file doesn't exist in the working directory.  What is the
>     command you're issuing (exact copy and paste from the terminal,
>     please)?  What are the contents of the working directory?
> 
>     -Justin
> 
>      >
>      > --- On *Mon, 1/31/11, Mr Bernard Ramos /<bgrquantum at yahoo.com
>     <http://us.mc527.mail.yahoo.com/mc/compose?to=bgrquantum@yahoo.com>>/*
>     wrote:
>      >
>      >
>      >     From: Mr Bernard Ramos <bgrquantum at yahoo.com
>     <http://us.mc527.mail.yahoo.com/mc/compose?to=bgrquantum@yahoo.com>>
>      >     Subject: Re: [gmx-users] luck
>      >     To: jalemkul at vt.edu
>     <http://us.mc527.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu>,
>     "Discussion list for GROMACS users"
>      >     <gmx-users at gromacs.org
>     <http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org>>
>      >     Date: Monday, January 31, 2011, 1:14 PM
>      >
>      >     thanks.
>      >               Here is the error i mentioned a while back with
>     using pdb2gmx:
>      >          ----------------------------------------------------------
>      >     File input/output error:
>      >     filename.pdb
>      >     For more information, visit ............
>      >     ----------------------------------------------------------
>      >     thanks for the time
>      >
>      >     --- On *Mon, 1/31/11, Justin A. Lemkul /<jalemkul at vt.edu
>     <http://us.mc527.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu>>/* wrote:
>      >
>      >
>      >         From: Justin A. Lemkul <jalemkul at vt.edu
>     <http://us.mc527.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu>>
>      >         Subject: Re: [gmx-users] luck
>      >         To: "Gromacs Users' List" <gmx-users at gromacs.org
>     <http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org>>
>      >         Date: Monday, January 31, 2011, 12:33 PM
>      >
>      >
>      >
>      >         Mr Bernard Ramos wrote:
>      >          > Do I need to type in g_luck instead?
>      >          >
>      >
>      >         Typing an email and waiting for a response takes far more
>     time
>      >         and effort than simply trying it yourself ;)
>      >
>      >         -Justin
>      >
>      >          > --- On *Mon, 1/31/11, Justin A. Lemkul
>     /<jalemkul at vt.edu
>     <http://us.mc527.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu>
>      >            <http://us.mc527.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu>>/*
>      >         wrote:
>      >          >
>      >          >
>      >          >     From: Justin A. Lemkul <jalemkul at vt.edu
>     <http://us.mc527.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu>
>      >            <http://us.mc527.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu>>
>      >          >     Subject: Re: [gmx-users] luck
>      >          >     To: "Discussion list for GROMACS users"
>      >         <gmx-users at gromacs.org
>     <http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org>
>      >            <http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org>>
>      >          >     Date: Monday, January 31, 2011, 12:11 PM
>      >          >
>      >          >
>      >          >
>      >          >     Mr Bernard Ramos wrote:
>      >          >      > Hi everyone!
>      >          >      >  I have two questions.
>      >          >      >  1. after I installed gromacs 4.5.3 and "which
>     mdrun"
>      >         was able to
>      >          >     give the correct path, I was not able to run "luck".
>      >         Instead, "luck"
>      >          >     gives an error "command not found". Is this ok?
>     What went
>      >         wrong? Do
>      >          >     I need to install again gromacs?
>      >          >      >
>      >          >     The program is now called g_luck.
>      >          >
>      >          >      > 2. I tried doing "pdb2gmx". The error points the
>      >         structure file
>      >          >     "*.pdb" as the error. Does this in dicate that the
>      >         program was not
>      >          >     installed properly or there is an error with the
>     pdb file.
>      >          >      >
>      >          >     If the program has given you a fatal error, then the
>      >         program is
>      >          >     correctly installed and working.  It is your input
>     that
>      >         is somehow
>      >          >     wrong.  Without the actual error message, it's
>     impossible
>      >         to say
>      >          >     what's wrong.
>      >          >
>      >          >     -Justin
>      >          >
>      >          >      >  Thanks
>      >          >      >
>      >          >
>      >          >     -- ========================================
>      >          >
>      >          >     Justin A. Lemkul
>      >          >     Ph.D. Candidate
>      >          >     ICTAS Doctoral Scholar
>      >          >     MILES-IGERT Trainee
>      >          >     Department of Biochemistry
>      >          >     Virginia Tech
>      >          >     Blacksburg, VA
>      >          >     jalemkul[at]vt.edu | (540) 231-9080
>      >          >        http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>      >          >
>      >          >     ========================================
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>      >
>      >         Justin A. Lemkul
>      >         Ph.D. Candidate
>      >         ICTAS Doctoral Scholar
>      >         MILES-IGERT Trainee
>      >         Department of Biochemistry
>      >         Virginia Tech
>      >         Blacksburg, VA
>      >         jalemkul[at]vt.edu | (540) 231-9080
>      >         http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>      >
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>     -- ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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-- ========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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