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

From: Nihal Korkmaz <>
Date: Wed, 15 Oct 2014 16:29:51 -0500

Thanks Hai,

I am using the correct force field, gb and radii combination. Amber
passed the tests as well. I just need to install the recent updates.

I think the root of my problems is either my equilibration step or small
rgbmax i have been using. I have been using 12 mainly to be able to run
faster. I will check how much difference it makes and simulate with a
larger rgbmax and equilibrate as described in the paper you mentioned.


On 10/15/14, 12:00 AM, Hai Nguyen wrote:
> Hi,
> 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"?
> Hai
> On Tue, Oct 14, 2014 at 4:50 PM, Nihal Korkmaz <>
> wrote:
>> 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
>> _______________________________________________
>> AMBER mailing list
> _______________________________________________
> AMBER mailing list

E. Nihal Korkmaz
UW-Madison, Biophysics Program
Qiang Cui Lab
Phone: 608-265-3644
AMBER mailing list
Received on Wed Oct 15 2014 - 15:00:02 PDT
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