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

[Justin A. Lemkul]

Aldo Segura wrote:
> Dear gmxusers,
> 
> I need to perform molecular dynamics simulation of a B2AR within the
> POPC membrane. I have downloaded the 128b.pdb, popc.itp and lipid.itp
> files from Prof.Tieleman's group. My protein of interest is 343
> residues. Also, I aligned the protein and membrane. I followed the
> Justin Lemkul tutorial for KALP-15. The result of inflate.gro is in
> agreement with the result showed in the tutorial (Visual inspection
> with VMD). However, the result of the first minimization shows that
> the protein and lipids are separated rather than starting to pack. I'm
> using gromacs-4.5.3.
> 
> Can someone help me?
> 

Energy minimization does not pack the lipids around the protein.  You have to do 
numerous iterations of shrinking + EM to accomplish this.  There is a protocol 
in the tutorial for this.  Or is there some other problem?

-Justin

> my minim.mdp file:
> 
> ; minim.mdp - used as input into grompp to generate em.tpr
> ; Parameters describing what to do, when to stop and what to save
> define		= -DSTRONG_POSRES ; position restrain the protein
> integrator	= steep		; Algorithm (steep = steepest descent minimization)
> emtol		= 1000.0  	; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
> emstep          = 0.01          ; Energy step size
> nsteps		= 50000	  	; Maximum number of (minimization) steps to perform
> 
> ; Parameters describing how to find the neighbors of each atom and how
> to calculate the interactions
> nstlist		= 1		; Frequency to update the neighbor list and long range forces
> ns_type		= grid		; Method to determine neighbor list (simple, grid)
> rlist		= 1.2		; Cut-off for making neighbor list (short range forces)
> coulombtype	= PME		; Treatment of long range electrostatic interactions
> rcoulomb	= 1.2		; Short-range electrostatic cut-off
> rvdw		= 1.2		; Short-range Van der Waals cut-off
> pbc		= xyz 		; Periodic Boundary Conditions (yes/no)
> 
> 
> 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

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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