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>> 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
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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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