Re: [AMBER] ff99SB*-ildn again

From: Jason Swails <jason.swails.gmail.com>
Date: Thu, 14 Jul 2016 09:58:00 -0400

On Thu, Jul 14, 2016 at 3:56 AM, Vlad Cojocaru <
vlad.cojocaru.mpi-muenster.mpg.de> wrote:

> Hi Neha,
>
> What you are saying argues against trusting conversion tools between
> Gromacs and Amber (its good you did a thorough test, but many don't do
> that) ....


‚ÄčI don't think that's what this shows. In fact, I think it would suggest
precisely the opposite -- i.e., you *should* trust conversion tools that
convert between topology formats (rather than raw parameter file formats)
where reasonably possible.

Ignoring the fact that these are different force fields for a minute, the
comparison made here is from a GROMACS-generated file converted to Amber
using ParmEd to a file created directly with Amber's tleap.

Particularly problematic are how different programs assign impropers --
they are very often assigned in different orders, and so result in
non-identical topologies. This is why it's very challenging to get a
GROMACS-generated file using ff99SB-ildn to agree perfectly with an
Amber-generated file using ff99SB-ildn.

By contrast, tools like ParmEd and InterMol take the exact topology defined
within either the GROMACS or Amber files and converts them faithfully into
the other format using the exact same atom ordering for every topological
feature. These tools *are* validated by comparing energies and forces
calculated by GROMACS and Amber and making sure they agree to the expected
level of precision (usually ~0.1 kcal or lower, depending on system size
and precision limits).

My experience is that I have a lot more confidence in a file converted from
the file format in which the original FF implementation was proposed into
another program's format than trusting that the underlying force field
parameter files were converted correctly *and* that each program's
respective parametrization tools makes the same choices in all situations.

In fact, I would use the former to help identify, quantify, and debug
problems in the latter.

All the best,
Jason

P.S., Of course, if you use different force fields in both programs, as was
done here, such a comparison is moot, anyway :)

-- 
Jason M. Swails
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Received on Thu Jul 14 2016 - 07:00:03 PDT
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