[gmx-users] preparing proteins for a peptide/bilayer MD sim

[kia balali]

Dear All,

Sorry for re sending this .....but I have not received a satisfactory 
response. Someone replied saying they have similar problems on how to insert 
their peptide into a bilayer, but that's all!

"In brief my main concern is whether it is acceptable to place a peptide in 
a box with NO solvent ...run an MD sim with standard parameters and then 
insert the peptide in a pre equilibrated hydrated bilayer?"

Having done MD sims with GROMACS for the last 1.5 years with various 
customized 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 it in an
equilibrated/hydrated bilayer. I don't see anything wrong..and haven't
experienced any crashes for once!!!!!!!!!!!

Please give me your brief thoughts on this....Your comments are very much 
appreciated!

Many thanks :-)

Kia Balali-Mood




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