[gmx-users] input/output error in production grompp

[Justin A. Lemkul]

On 6/13/12 9:11 AM, Malai wrote:
> Hello Justin,
>
> Thanks for reply. After getting this, I started to run production run but here i
> didnt get any error. so is it OK? or still I need to look at this error? Thanks
>

What's anomalous to me is that grompp produced an I/O error (referencing an 
unused or nonexistent file) but still produced a .tpr file.  Fatal errors 
prevent grompp from working, so you shouldn't have gotten a .tpr file in this 
case.

You need coordinates in the .tpr file to work, but if you did in fact use a .pdb 
file, then the .tpr is fine.  The reference to the .gro file is still a complete 
mystery to me.

-Justin

> On Wed, Jun 13, 2012 at 8:35 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
>     On 6/13/12 8:27 AM, Malai wrote:
>
>         HI,
>
>         Sorry for wrongly typing. The command I issued is:  grompp -v -f hex1.mdp -c
>         hex1.pdb -p hex1.top -o hex1.tpr.
>
>         The error is bellow:
>
>
>         Error:
>         Program grompp, VERSION 4.5.4
>         Source code file: futil.c, line: 491
>
>         File input/output error:
>         hex1.gro
>         For more information and tips for troubleshooting, please check the GROMACS
>         website at http://www.gromacs.org/____Documentation/Errors
>         <http://www.gromacs.org/__Documentation/Errors>
>         <http://www.gromacs.org/__Documentation/Errors
>         <http://www.gromacs.org/Documentation/Errors>>
>
>
>     Even with the corrected command, I see no way for this error to come up.
>       There is no reference to a .gro file anywhere in your command.
>
>
>     -Justin
>
>     --
>     ==============================__==========
>
>     Justin A. Lemkul, Ph.D.
>     Research Scientist
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 <tel:%28540%29%20231-9080>
>     http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>     <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
>     ==============================__==========
>
>
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-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================