Re: AMBER: Simulations with GB models

From: Carlos Simmerling <>
Date: Thu, 11 Jan 2007 13:28:16 -0500

I don't think this is a technical issue, it is more likely a question
of the science involved with implicit water models and whether
they are a good model for low-temperature experiments with
crystal packing. You should read the literature and see
if people have used GB models to do the kind of studies
that interest you. For example, we recently compared explicit water
and GB simulations of peptides, you might read that as well as the
work by others that we reference. People go to a lot of effort
to write and to review articles, so it's not really practical
to go through it all here on the email server. If you technical problems
getting Amber or GB to work, we'd be happy to help out.
If you wanted you could use restraints to hold the chains together,
but I'm not sure what you would learn since you are forcing them
to do it. Check the NMR distance restraint section of the manual
if you want to try that.
good luck!

**Mongan, J., Simmerling, C., McCammon, J. A., Case, D.and Onufriev, A.,
/Generalized Born model with a simple, robust molecular volume
correction/, J. Chem. Theory & Comput., 3:156-169 (2007)

**Okur, A., Wickstrom, L., Layten, M., Geney, R., Song, K., Hornak, V.
and Simmerling, C., /“Improved Efficiency of Replica Exchange
Simulations through Use of a Hybrid Explicit/Implicit Solvation Model”/,
J. Chem. Theory Comput., 2:420, 2006.

Wei Chen wrote:

> Hi, all,
> I try to simulate a protein with two peptide chains using Amber8. Due
> to the big size of the system, I have to use implicit water. I choosed
> a General Born model (igb=2). I set cutoff 15A, salt concentration
> 0.1M. I also use SHAKE and set dt 2 fs. First, I minimized the system
> for 10,000 steps. Then heat up the system from 0 to 300K in 20ps. In
> the crystal structure, the two peptide chains associate with each
> other by non-covalent interaction. However, during the heat-up and
> following production run, two peptide chains wander apart more and
> more. Finally, they separate totally in 40ps. I don't think this is
> the real. My question is why the two peptide chains separate when
> using General Born model. Is there anyway to overcome this problem to
> hold two chains together?
> Thank you!
> Wei Chen
> Control Parameters:
> molecular dynamics run with implicit water
> &cntrl
> imin=0, irest=1, ntx=5,
> nstlim=44500, nmropt=1,
> ntpr=100, ntwx=500, ntwr=500,
> cut=15.0, ntb=0,
> ntr=0, ntt=1, ntp=0,
> igb=2, saltcon= 0.1,
> ntc=2, dt=0.002,
> /
> #
> #heat up and equilibrium algorithm:
> #
> #from steps 0 to 50000: heat the system to 300K
> #from steps 50001-200000: leave at 300K
> #
> &wt type='TEMP0', istep1=0,istep2=4500,value1=138.,
> value2=300., /
> &wt type='TEMP0', istep1=4501, istep2=44500, value1=300.0,
> value2=300.0, /
> &wt type='TAUTP', istep1=0, istep2=44500,value1=1.0,
> value2=1.0, /
> &wt type='END' /

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Received on Sun Jan 14 2007 - 06:07:30 PST
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