[gmx-users] Error in protein insertion in bilipid layer

[Justin Lemkul]

On 12/8/14 2:47 AM, Priya Das wrote:
> Dear All,
>
> After insertion of my big proteinin lipid bilayer (512) moleules, i used
> the command :
>
> perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat
>
> I get a area/ lipid : 10.231 nm2 and on shrinking i get 6. 89nm 2
> after only 9 rounds of simulation.
>
> But In the tutorial its around 26 rounds of iteration.
>
> After this step when i solvate the system, there is a cavity at the
> interface of hydrophobic region of protein and t
>
> the membrane. There are a large number of unwanted water molecules
> which i cannot delete manually.
>
> Is there any mistake in inflate step; i mean nanometer and angstrom scale?
>

6.89 nm^2 is 689 A^2, not 68.9.  Mind the square in the units.  You need more 
packing steps because you are not anywhere near close enough to a sensible APL.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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