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

[Priya Das]

Oops ....i am sorry

On Mon, Dec 8, 2014 at 6:05 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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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-- 
*Let us all join hands to save our " Mother Earth"*
------------------------------------------------------------------------
Regards,
Priya Das
Research Scholar
Dept. of Computational Biology and Bioinformatics,
University of Kerala