[gmx-users] Lipid Bilayer questions

[Dallas Warren]

>1) Which is the best force field to use for a DMPC bilayer?

Probably either OPLS-AA or G43a2.

>2) If i used the DMPC.itp from Dr Tieleman s site, where do i need to save 
>it in
>order for the pdb2gmx,edit conf etc to work....that is, do i need to save 
>it in
>the "top" folder or do i need to place it in the specific forcefield file for
>it to work?

The *.itp file is used in the simulation steps (whether that is energy 
minimisation, restrained simulation and full run).  So it only has to be in 
the paths or the current working directory.

>3) How do i create a DMPC.top file and DMPC.gro file? (I mean are there any
>DMPC.pdb files out there?)

For the .top file, see the manual.  For the .gro file, if you want a single 
molecule, you can just take the .gro file for the membrane and copy out a 
single molecule from that.

>4) I tried using pdb2gmx on Dr Tieleman s DPPC64.pdb,and ended up getting 26
>(A-Z) posre.itp files and DPPC_A.itp -DPPC_Z.itp(ANother 26).Is it 
>necessary to
>create all these files seperately? BUt since there are 64 lipids, what about
>the other lipids? Is it necessary to create posre files for every individual
>lipid?

You only need one posre file for each type of molecule, not for each molecule.

>5) Are there any good resources out there which describe how to setup a 
>bilayer
>simulation,Since i am working this out all on my own, i dont have anyone to
>discuss this with.

Search this emailing list, has been discussed in various manners for some 
time.  Plus read any publications to find out how others are doing things.

Catch ya,

Dr. Dallas Warren
Lecturer
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9083
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