[gmx-users] Simulation of membrane protein

[Justin A. Lemkul]

James Starlight wrote:
> Thanks, Justin
> I'll test your program soon.
> 
> Today also I have some problems with generation of the posre for lipids
> 
> I have lipid bilayer in pdb. Then I selected one lipid molecule and move 
> it to  separate pdb and convert it to gro via editconf.
> Than I've used genres and generate posre file for 1 lipid. Than I 
> include tis posre to topology of my bilayer
> using gropt I obtain eror that I'm using wrong posre topology
> 
> Also I've tried to include posre.itp to my lipid.itp ( this file contain 
> link to posre on default) This run didnt produce any errors but as the 
> result posres have not been worked ( I obtained perturbed bilayer after 
> minimization)
> 
> How I can generate work posre for my bilayer to prevent perturbation 
> after equilibration or minimization ?
> 

Since posre.itp is the default name given to the protein position restraint file 
by pdb2gmx, the first step is to use a different name.  Then, you have to add 
the new #include statement in the correct location in the topology.  Presuming 
you do that, the lipids should be restrained in whatever manner you've specified.

-Justin

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

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

========================================