AMBER Archive (2003)

Subject: Re: AMBER: Simulation of small protein

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Thu Oct 23 2003 - 11:13:09 CDT

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
though.

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?)
Carlos

----- Original Message -----
From: "Endres, Robert G." <endresrg_at_ornl.gov>
To: <amber_at_scripps.edu>
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
kcal/mol.
> 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
structure?
>
> Many thanks for suggestions,
>
> Robert
>
>
>
>
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