[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
>
> ========================================
> -- gmx-users mailing list gmx-users at gromacs.org
> <http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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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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