[gmx-users] Help with B2AR within the POPC membrane

Justin A. Lemkul jalemkul at vt.edu
Wed Feb 9 00:21:17 CET 2011

Aldo Segura wrote:
> Thanks for your answer. You're right in the procedure for the packing
> of the protein and lipids. However, after several iterations (~30) the
> lipids are packaged to form the bilayer and the protein is outside of
> it. I can send you a couple of pictures for a better explanation of my
> problem.

That typically happens when either (1) the box vectors are not set correctly 
during system construction or (2) the protein is not properly positioned in the box.


> Best regards,
> Aldo Segura-Cabrera
> Laboratorio de Bioinformática
> Centro de Biotecnología Genómica
> Instituto Politécnico Nacional
> Blvd. Del Maestro esquina Elías Piña, 88710
> Reynosa, Tamaulipas, México.
> (899)9243627 ext. 87747
> e-mail: asegurac at ipn.mx; aldosegura at gmail.com


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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