On 6/13/12 9:22 AM, Malai wrote:
HI Justin,

I did use the .pdb file as I showed in the grompp command. If I got I/O error,
the mdrun should not work? but here the mdrun is working. Thanks.


As I said before, if the .tpr file was produced, there was no problem. The error message makes no sense at all to me.

-Justin

On Wed, Jun 13, 2012 at 9:14 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:



    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 <jalem...@vt.edu
        <mailto:jalem...@vt.edu>
        <mailto:jalem...@vt.edu <mailto:jalem...@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>>

                <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
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            Virginia Tech
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    --
    ==============================__==========

    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
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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

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