Please note there is no evidence here of a "pmemd" problem (ie., pmemd doing
something different than the reference sander implementation). So this is a
question first for the gb folks. If it turns out that pmemd is doing
something different for some particular collection of input parameters/data,
though, I would of course like to know!
Regards - Bob Duke
----- Original Message -----
From: "Sampath Koppole" <sampathkoppole.yahoo.com>
To: <amber.scripps.edu>
Sent: Thursday, September 25, 2008 5:09 AM
Subject: AMBER: Amber GB problems on PMEMD !!
> 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.
>
> --
> *****************************************************************
> Dr. Sampath Koppole,
> Horburgstr. 35
> CH 4057 Basel
> Switzerland.
> Ph: +41-76-422-8100
> *****************************************************************
>
>
>
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Received on Fri Sep 26 2008 - 05:10:25 PDT
