Re: [AMBER] Loss of secondary structure in GB simulations

From: Hai Nguyen <>
Date: Wed, 15 Oct 2014 01:00:49 -0400


it's likely there is something wrong with your protocol. I am not surprised
if protein unfold quickly in GB7 but we did have simulation for Ubiquitin
with 14SBonlysc + GB8 (PDB: 1UBQ) and it's very stable in our simulation at
300K (>10 us). We have just published a paper showing using this force
field and solvent model with different topology, in both REMD and MD. You
might want to check out (see supporting information)

You might want to double-check if you really used ff14SBonlysc or not. What
is radii for GB8 (should be mbondi3). Did the AMBER pass the test?

Look at your your md input, I think you used very small value of
"rgbmax=12". You should use the default one.

PS: did Ubiquitin unfold and turn alpha helix or just "unfold"?


On Tue, Oct 14, 2014 at 4:50 PM, Nihal Korkmaz <>
> Dear all,
> I have been running ff99SBnmr+gb7 and ff14SBonlysc+gb8 simulations. For
> only alpha helical systems I do not have any problems. However, with
> proteins that also contain B-sheets I observe high RMSD values and loss
> of secondary structure, mostly B-sheets. This is not only happening
> after simulating for a long time but I observe a steady increase in
> RMSD. For Ubiquitin monomer, I have 5 AA Calpha-RMSD at 70 ns, it
> reaches up to 10.5 AA and the Ub fold is lost.
> I am wondering if anyone experienced the same and has a suggestion to
> fix this.
> This is my input file:
> &cntrl
> imin=0, ntb=0, ntx=5, irest=1,
> ntpr=1000, ntwr=10000000, ntwx=1000, ntwe=5000,
> nstlim=10000000, dt=0.001,
> ntt=3, temp0=300.00, tempi=300.00,
> ig=-1, tautp=1, gamma_ln=20,
> ntc=2, tol=0.00001, ntf=2,
> dielc=1, cut=9999, rgbmax=12,
> igb=8, gbsa=0,
> saltcon=0.15, ioutfm=1, nscm=100,
> &end
> Thanks
> --
> E.N. Korkmaz
> UW-Madison, Biophysics Program
> _______________________________________________
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Received on Tue Oct 14 2014 - 22:30:03 PDT
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