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 /<[email protected]>/* wrote:
From: Justin A. Lemkul <[email protected]>
Subject: Re: [gmx-users] luck
To: "Discussion list for GROMACS users" <[email protected]>
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 /<[email protected]
<http://us.mc527.mail.yahoo.com/mc/[email protected]>>/*
wrote:
>
>
> From: Mr Bernard Ramos <[email protected]
<http://us.mc527.mail.yahoo.com/mc/[email protected]>>
> Subject: Re: [gmx-users] luck
> To: [email protected]
<http://us.mc527.mail.yahoo.com/mc/[email protected]>,
"Discussion list for GROMACS users"
> <[email protected]
<http://us.mc527.mail.yahoo.com/mc/[email protected]>>
> 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 /<[email protected]
<http://us.mc527.mail.yahoo.com/mc/[email protected]>>/* wrote:
>
>
> From: Justin A. Lemkul <[email protected]
<http://us.mc527.mail.yahoo.com/mc/[email protected]>>
> Subject: Re: [gmx-users] luck
> To: "Gromacs Users' List" <[email protected]
<http://us.mc527.mail.yahoo.com/mc/[email protected]>>
> 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
/<[email protected]
<http://us.mc527.mail.yahoo.com/mc/[email protected]>
>
<http://us.mc527.mail.yahoo.com/mc/[email protected]>>/*
> wrote:
> >
> >
> > From: Justin A. Lemkul <[email protected]
<http://us.mc527.mail.yahoo.com/mc/[email protected]>
>
<http://us.mc527.mail.yahoo.com/mc/[email protected]>>
> > Subject: Re: [gmx-users] luck
> > To: "Discussion list for GROMACS users"
> <[email protected]
<http://us.mc527.mail.yahoo.com/mc/[email protected]>
>
<http://us.mc527.mail.yahoo.com/mc/[email protected]>>
> > 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
> >
> > ========================================
> > -- gmx-users mailing list [email protected]
<http://us.mc527.mail.yahoo.com/mc/[email protected]>
>
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> >
<http://us.mc527.mail.yahoo.com/mc/[email protected]>
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search
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> > Please don't post (un)subscribe requests to the
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>
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> >
<http://us.mc527.mail.yahoo.com/mc/[email protected]>.
> > Can't post? Read
http://www.gromacs.org/Support/Mailing_Lists
> >
> >
>
> -- ========================================
>
> 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 [email protected]
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>
<http://us.mc527.mail.yahoo.com/mc/[email protected]>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search
before posting!
> Please don't post (un)subscribe requests to the list. Use the
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>
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>
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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 [email protected]
<http://us.mc527.mail.yahoo.com/mc/[email protected]>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to [email protected]
<http://us.mc527.mail.yahoo.com/mc/[email protected]>.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
========================================
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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