[gmx-users] Question Re. KALP-15 in DPPC tutorial

[jhosamelly]

I got into this part of the KALP-15 in DPPC 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"):

perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat

Follow this up by another round of EM. During the "shrinking" steps, be sure to change the cutoff value to 0, or else you will continue to delete lipids! After 26 iterations of scaling down by 0.95, I reached an area per lipid of ~71 Å2, above the experimental value of ~62 Å2. Since the script tends to overestimate the area per lipid, this value is good enough to continue to equilibration."

I added the line at the topol.top [molecule]
DDPC     126
Then I tried
grompp -f minim.mdp -c system_inflate.gro -p topol.top -o em.tpr -maxwarn 1

Somehow, it worked. But I didn't get any confout.gro file so the 

perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat

doesn't work.

Melsa Rose Ducut


> On Jan 25, 2014, at 12:41 PM, "Justin Lemkul [via GROMACS]" <ml-node+s5086n5014038h72 at n6.nabble.com> wrote:
> 
> 
> 
> On 1/24/14, 11:21 PM, jhosamelly wrote:
> 
> > 
> > Thanks Justin. I fixed the problem earlier but when I got to 
> > 
> > "2. Pack the lipids around the protein 
> > 
> > The easiest method I have found so far for packing lipids around an embedded 
> > protein is the InflateGRO methodology (ref), available here. First, 
> > concatenate the protein and bilayer structure files: 
> > 
> > cat KALP_newbox.gro dppc128_whole.gro > system.gro 
> > 
> > Remove unnecessary lines (the box vectors from the KALP structure, the 
> > header information from the DPPC structure) and update the second line of 
> > the coordinate file (total number of atoms) accordingly." 
> > 
> > I don't know what file to edit. Remove unnecessary lines in what file?
> 
> In system.gro.  If you study the file format and examine what you have created, 
> you will see that there is extraneous stuff that will break the file format. 
> 
> -Justin 
> 
> -- 
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> Justin A. Lemkul, Ph.D. 
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> 
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