RE: AMBER: Simulation of small protein

From: Endres, Robert G. <>
Date: Thu, 23 Oct 2003 13:27:45 -0400

Dear Carlos,
its the villin headpiece which was described as a thermostable, fast folding
alpha-helical subdomain. I also looked at the trajectory with mddisplay: at the beginning of the movie the structure seems a bit more open, but its hard to tell since its just a bunch of wobbling atoms.

What's a better force field - parm94, or the one you published
in JACS on Trpcage folding? By the way, in this paper did you use GB or GBSA?
When I just use GB (without SA-term) it actually partially unfolds at the beginning of trajectory (starts to open up but closes then slowly again).


-----Original Message-----
From: on behalf of Carlos Simmerling
Sent: Thu 10/23/2003 12:13 PM
Subject: Re: AMBER: Simulation of small protein
it depends on whether you're seeing backbone changes-
we've publsihed that there is significant overstabilization of alpha
helix in parm99+GB. on a long time scale, all of
our sequences increased in helical content and the
energy dropped. Seeing this during 200ps is a bit surprising

without knowing what the topology looks like it is
hard to say whether more compact is reasonable (is it
a rather open structure to start with?)

----- Original Message -----
From: "Endres, Robert G." <>
To: <>
Sent: Thursday, October 23, 2003 11:52 AM
Subject: AMBER: Simulation of small protein

> Dear AMBER users,
> After heating/equilibration of a NMR structure of a small (36 res.)
protein with weak constraints, I was doing a short (0.2 ns) MD simulation
(parm99.dat) at 300K with the GBSA implicit solvent model.
> I was a bit surprised that the total energy dropped further by almost 100
kcal/mol compared to the starting structure (close to NMR structure), and
the ESURF term (proportional to the total surface) decreased from 17 to 12
> So the protein got more compact during the MD simulation. The RMSD started
from zero and increased to 3-5 A.
> It seems that the protein changed quite strongly the structure during the
simulation. Does anyone have experience with this, i.e. is this "normal" or
"expected", is this a problem with the force field/solvent model or NMR
> Many thanks for suggestions,
> Robert
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Received on Thu Oct 23 2003 - 18:53:00 PDT
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