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

[Mark Abraham]

On 25/01/2012 9:32 PM, 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!
>
> 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"):".

Apparently you did the EM too late, or it broke. Check the order of your 
operations and pay attention to warnings and errors.

Mark
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