AMBER Archive (2008)

Subject: Re: AMBER: Amber GB problems on PMEMD !!

From: Sampath Koppole (sampathkoppole_at_yahoo.com)
Date: Thu Sep 25 2008 - 08:02:42 CDT

Dear Bob Duke,
I am sorry. I did not mean to indicate that there is a problem with pmemd. I just wanted to tell that I was using pmemd for all these tests.

Just to add an other note to my previous email: My tests on Villin head and GB1 (PDB id : nug2) using mbondi and igb7 seem quite good but bondi and igb=7 seem too-solvated and the protein seem to be falling apart (this is 1 ns of MD of the native state)

Is there a publication which suggests the best gb method in Amber ?

Thanks a lot for your time.
With best regards,
Sampath.

--- On Thu, 9/25/08, Robert Duke <rduke_at_email.unc.edu> wrote:

> From: Robert Duke <rduke_at_email.unc.edu>
> Subject: Re: AMBER: Amber GB problems on PMEMD !!
> To: amber_at_scripps.edu
> Date: Thursday, September 25, 2008, 2:22 PM
> 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_at_yahoo.com>
> To: <amber_at_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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