[gmx-users] Query regarding energy minimization for packing the lipids around the protein

Justin A. Lemkul jalemkul at vt.edu
Wed Jan 25 14:17:43 CET 2012

Anushree Tripathi wrote:
> I have used "mdrun -v deffnm em" command for energy minimization just 
> after running the command i.e., given below:
>  perl inflategro.pl <http://inflategro.pl> system.gro 4 DPPC 14 
> system_inflated.gro 5 area.dat
> But When I run the command which is given below:
> Eeeeek! No confout.gro at all!

That could not have been the command you entered, because inflategro.pl is 
looking for confout.gro, which you have not specified in the command.  Please 
copy and paste directly from the command line, rather than try to remember what 
you did or just copy from the tutorial.

> Died at inflategro.pl <http://inflategro.pl> line 81.
> Please guide me to troubleshoot the error.
> Also clarify the lines given in tutorial "Note how many lipids were 
> deleted and update the |[ molecules ]| directive of your topology 
> accordingly. Run energy minimization. Then, scale down the lipids by a 
> factor of 0.95 (assuming you have used default names, the result of the 
> minimization is called "confout.gro"):".

Think about what inflategro.pl is doing - it is removing lipids from your 
coordinate file.  Thus the original topology that specifies a protein and 128 
DPPC lipids is no longer correct.  The screen output tells you how many lipids 
were removed.  Use that information to update the [molecules] directive to 
accurately reflect what now remains in your system.



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


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