Dear All,
I have been trying to use GB implementations that are available in PMEMD.
I decided to use the GB model implemented by Mongan, Simmerling, McCammon,Case and Onufriev (igb=7). I first used the recommended bondi radii while creating my prmtop file (set default PBradii bondi) with leaprc.ff03.
I then ran 80 ns simulation on a small 20 amino-acid protein TRP cage (PDB id : 2jof.pdb) as a test case. This protein completely unfolds and folds again within this time-scale (80 ns). Experimentally this small peptide is supposed to fold in 4 micro-seconds or so (in explicit water).
I then tried the default born radii, mbondi. I changed all the Hydrogen born radii which were 0.8 to 1.0 by hand to make it work with igb=7, otherwise, it does not work !!
I find the system very stable with mbondi radii (the protein does not unfold, while the unfolded protein does not fold) in 80 ns. The native structure remains within 3.5 Ang RMSD (on all heavy atoms).
To confirm this behavior behavior, I also tried the same thing with another protein, the vilin head (36 amino acids), PDB id: 1VII.pdb with bondi radii. The protein infact begins to unfold in 1 ns (RMSD goes to 6 A in 1 ns, on all heavy atoms). I have not done the folding simulation starting from an unfolded vilin head.
Could any one please guide me which is the best force-field settings to use igb=7 implicit solvent with pmemd.
Thanks a lot,
Cheers,
Sampath.
--
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Dr. Sampath Koppole,
Horburgstr. 35
CH 4057 Basel
Switzerland.
Ph: +41-76-422-8100
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Received on Fri Sep 26 2008 - 05:10:02 PDT
