[AMBER] Loss of secondary structure in GB simulations

From: Nihal Korkmaz <enihalkorkmaz.gmail.com>
Date: Tue, 14 Oct 2014 15:50:13 -0500

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:
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,


E.N. Korkmaz
UW-Madison, Biophysics Program
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Received on Tue Oct 14 2014 - 14:00:03 PDT
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