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

[kia balali]

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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