Re: [AMBER] Using polarized force field lead to large RMS in the second step of minimization

From: David A Case <>
Date: Thu, 14 Aug 2014 08:44:38 -0700

On Thu, Aug 14, 2014, 张冬冬 wrote:

> Recently, I've been working on a job about using a polarized
> FF(leaprc.ff02) to simulate a protein-nanotube system(model
> processing is as A00). When I run minimization of step one, mdout
> results seemed to be fine(A01). When I went to step two, however,
> I found that the RMS and dipole convergence rms became very
> large(The mdout file is as below A02. ). With many uncertainties
> I went on with the minimization of step three, and I shockingly
> found that the RMS and dipole convergence rms turns out to be too
> large to see(The mdout file is as below A03)!! I have tried many
> different combinations of namelists in the $cntrl, leading to the
> same results. When I turned to the amber tutorials hoping to find
> some helpful answers but I got nothing related to this. So, could
> you help me with this? All in all, I hope you can give me some
> suggestions about using amber polarized FF.

There is not much to go on here: we don't know how you are describing the
nanotube, or what behavior you expect. The two pretty obvious caclulations to
try are these:

1. Do a calcuation of just the protein in ff02 (You should use the ".R1"
version, e.g. "source oldff/leaprc.ff02pol.r1". I don't know where you got
leaprc.ff02 from, perhaps an old version of Amber? Note that the "oldff"
designation means that these force field is no longer supported or
recommended, and is only provided if comparisons to old simulations are
needed.) See if a simple system (perhaps even a peptide) works the way you
hope it will. This will help eliminate possible problems with the nanotube

2. Do a calculation with a non-polarizable potential. This will help make
sure that the system is working OK (or not) in the absence of polarizability.

Upgrading to the current version of Amber will make it much easier for people
on the list to provide help.


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Received on Thu Aug 14 2014 - 09:00:02 PDT
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