[gmx-users] luck
Mr Bernard Ramos
bgrquantum at yahoo.com
Tue Feb 1 19:29:40 CET 2011
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
--- 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>/* wrote:
>
>
> From: Mr Bernard Ramos <bgrquantum at yahoo.com>
> Subject: Re: [gmx-users] luck
> To: jalemkul at vt.edu, "Discussion list for GROMACS users"
> <gmx-users at 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>/* wrote:
>
>
> From: Justin A. Lemkul <jalemkul at vt.edu>
> Subject: Re: [gmx-users] luck
> To: "Gromacs Users' List" <gmx-users at 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>>/*
> 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: "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, 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
>
> ========================================
> -- gmx-users mailing list gmx-users at gromacs.org
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> 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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