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]>/* wrote:
From: Mr Bernard Ramos <[email protected]>
Subject: Re: [gmx-users] luck
To: [email protected], "Discussion list for GROMACS users"
<[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]>/* wrote:
From: Justin A. Lemkul <[email protected]>
Subject: Re: [gmx-users] luck
To: "Gromacs Users' List" <[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]>>/*
wrote:
>
>
> From: Justin A. Lemkul <[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]>>
> 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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