[gmx-users] Cutoff value during lipid shrinking using inflategro.pl script

Justin A. Lemkul jalemkul at vt.edu
Sat Apr 24 13:27:39 CEST 2010

Jignesh Patel wrote:
> Hello all,
> I am trying to do shrinking of lipids using inflategro.pl 
> <http://inflategro.pl> script. So anyone can suggest me *how much cut 
> off value* should I give to remove overlapped lipid residues. I have to 
> give *cutoff from starting step or at final step* of shrinking. 

You shouldn't be removing lipids when scaling your system down.  If you do, 
you'll keep deleting lipids until you have none left.

Have you gone through my membrane protein tutorial?  In it, I describe exactly 
how I usually go about running InflateGRO.



> perl    inflategro.pl <http://inflategro.pl>    confout.gro    0.95   
>  DPPC *   0   * system_shrink1.gro     5      area_shrink1.dat
> Thanking You in anticipation.
> -- 
> Best Wishes,
> Jignesh Patel
> M.S.(Pharm.),
> Center for Pharmacoinformatics,
> S.A.S. Nagar,
> India


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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