[gmx-users] Re: Doubt regarding membrane protein in POPC bilayer

Pawan Kumar pawan.chinari at gmail.com
Mon Mar 23 13:41:29 CET 2009

Respected Sir,

Thanks for all your help.
I will try this out and if I have any further queries I will ask you.
Thanks a lot.

Thanking you,

On Mon, Mar 23, 2009 at 5:58 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

Pawan Kumar wrote:

> Respected Sir,
> Thanks for all your help, suggestions and guidance.
> I have few more queries.
> Which type of box is appropriate in editconf - cubic or triclinic ?

That depends entirely upon the dimensions of your system and what is
adequate to accommodate the size of your embedded protein.

 I have read in one of your mails in the archives that POPE bilayer contains
> some bad interactions. As it contains more no. of lipids (340) it covers the
> full protein ( trimer which I am working on ) other than the few loop
> regions. How far that bilayer can be used or is it fine to use the biger
> bilayer of popc128a whcih I obtained by genconf ?
The choice of lipid should not be based on a size convenience.  It should be
based on a valid model system, and experimental evidence to which you can
correlate your results, if possible.

POPE presented a terrible challenge, since during the in vacuo InflateGRO
minimizations, the headgroups folded in on themselves to form intra-molecule
hydrogen bonds that resulted in a collapse of the molecule.  The solution
was to use freeze-grps in all dimensions during these minimizations, and
then equilibrate very carefully.

>> Justin A. Lemkul
>> Graduate Research Assistant
>> ICTAS Doctoral Scholar
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>> ========================================
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