[gmx-users] preparing a protein for sim with bilayers

[Osmany Guirola Cruz]

Hi 
 I have a similar problem with bilayers . i don't know how put my peptide in 
the bilayer. 


On Wednesday 19 March 2003 12:48, kia balali wrote:
> Dear All,
> Thanks to all who have replied to me before ..either on the list or
> personal emails...i'll address all queries to the list from now on!
> In addition i'll put all the data..bilayers with explicit hydrogens onto a
> website and email once i've got stuff published and finished my PhD!
> (another year...me hopes!)
> Having done MD sims with GROMACS for the last 1.5 years with bilayers ,I'm
> now planning to insert a alpha helical peptide in the headgroup region of
> the equilibrated bilayer. I was wondering if Drs. Lindahl, Van der Spoel,
> Tieleman etc....could comment on my protocol!
> 1. I took a PDB of the protein ..and ran it through pdb2gmx with ffgmx2
> 2. I added counter ions and linked them into the topology
> 3. I did a steep EM
> 4. I placed it in a triclinic box with NO solvent and  did an MD
> run....with PBC coulomb cut-off berendsen temp & press coupling
> 5. I plan to take this structure and place it onto the surface of an
> equilibrated bilayer
>
> The peptide now has a pot. energy of -5671.45 kj/mol is reasonbly
> stable....I would've used the gromos forcefield for vacuum....but it
> doesn't do explicit hydrogens...hence no use to me....I didn't want to
> solvate the peptide as it would affect it's structure before I place ina
> equilibrated/hydrated bilayer. I don't see anything wrong..and haven't
> experienced any crashes for once!!!!!!!!!!!
>
> Many thanks :-)
>
> Kia Balali-Mood
> Dept. of preclinical Veterinary Sciences
> Laboratory of Membrane Biophysics
> The Vet School
> Faculty group of Medicine & Veterinary Medicine
> University of Edinburgh
> Summerhall
>
>
>
>
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