[gmx-users] Re: Concerning a Fatal Error!

Justin Lemkul jalemkul at vt.edu
Sat Oct 13 22:30:51 CEST 2012

On 10/13/12 9:49 AM, Arman Mahboubi Soufiani wrote:
> Dear Justin,
> The followings are the two successive commands I used:
> *grompp -f justPLA.mdp -c 20LA-2layer-4chains.gro -p t-PLA.top -o
> justPLA-em.tpr
> mdrun -deffnm justPLa-em*

These commands would not produce the error posted previously.  The error would 
have resulted from:

mdrun -deffnm justPLA-em.tpr

The fact that the capitalization is different and the nature of the suffix 
supports this conclusion.  It is better to copy directly from the terminal 
rather than try to recreate what you did.  In any case, proper invocation of the 
command should solve the issue.  mdrun is looking for an .xvg file containing 
parameters for a tabulated dihedral; it needs to be named appropriately to 
function correctly.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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