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)
http://pubs.acs.org/doi/abs/10.1021/ja5032776
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 <enihalkorkmaz.gmail.com>
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
>
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Received on Tue Oct 14 2014 - 22:30:03 PDT
