[gmx-users] luck

[Mr Bernard Ramos]

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
------------------------------------------ 


--- 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>/* 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: 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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