<div class="gmail_quote">HI Justin,</div><div class="gmail_quote"><br></div><div class="gmail_quote">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. </div>
<div class="gmail_quote"><br></div><div class="gmail_quote">On Wed, Jun 13, 2012 at 9:14 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="im"><br>
<br>
On 6/13/12 9:11 AM, Malai wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hello Justin,<br>
<br>
Thanks for reply. After getting this, I started to run production run but here i<br>
didnt get any error. so is it OK? or still I need to look at this error? Thanks<br>
<br>
</blockquote>
<br></div>
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.<br>
<br>
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.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
On Wed, Jun 13, 2012 at 8:35 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a><br></div><div class="im">
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
On 6/13/12 8:27 AM, Malai wrote:<br>
<br>
HI,<br>
<br>
Sorry for wrongly typing. The command I issued is: grompp -v -f hex1.mdp -c<br>
hex1.pdb -p hex1.top -o hex1.tpr.<br>
<br>
The error is bellow:<br>
<br>
<br>
Error:<br>
Program grompp, VERSION 4.5.4<br>
Source code file: futil.c, line: 491<br>
<br>
File input/output error:<br>
hex1.gro<br>
For more information and tips for troubleshooting, please check the GROMACS<br></div>
website at <a href="http://www.gromacs.org/____Documentation/Errors" target="_blank">http://www.gromacs.org/____<u></u>Documentation/Errors</a><br>
<<a href="http://www.gromacs.org/__Documentation/Errors" target="_blank">http://www.gromacs.org/__<u></u>Documentation/Errors</a>><div class="im"><br>
<<a href="http://www.gromacs.org/__Documentation/Errors" target="_blank">http://www.gromacs.org/__<u></u>Documentation/Errors</a><br>
<<a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/<u></u>Documentation/Errors</a>>><br>
<br>
<br>
Even with the corrected command, I see no way for this error to come up.<br>
There is no reference to a .gro file anywhere in your command.<br>
<br>
<br>
-Justin<br>
<br>
--<br></div>
==============================<u></u>__==========<div class="im"><br>
<br>
Justin A. Lemkul, Ph.D.<br>
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Virginia Tech<br>
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==============================<u></u>==========<br>
<br>
Justin A. Lemkul, Ph.D.<br>
Research Scientist<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
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