[gmx-users] Simulation of membrane protein

Justin A. Lemkul jalemkul at vt.edu
Mon Oct 31 16:33:11 CET 2011

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 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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