Re: [AMBER-Developers] Third release candidate for AmberTools 1.5

From: Jason Swails <jason.swails.gmail.com>
Date: Sun, 27 Mar 2011 12:51:53 -0700

Hi Dave, everyone,

I decided to throw a little (not much) time at validating ff10 wrt what's
written in the manual. I've written a little script to do this (attached
here).

It runs a couple "stupid" calculations, just setting up systems with a wide
variety of different residues so I can make sure that I get as many of the
possible parameters represented as possible.

It builds identical prmtop files for ff99SB/ff10, and identical prmtop files
for ff99bsc0 for and RNA and DNA system. It then runs a very short MD on
each, and compares the mdout files.

As expected, the only ones that match (and match exactly through 100 steps)
is the ff10/ff99SB for proteins (good news, no?).

For the other ones, I don't know what frcmods to load on top of ff99bsc0 in
order to get what's "expected" for ff10.

Therefore, these will be a little bit more difficult to validate, but I hope
I've made it easier. The script will also generate frcmod files extracted
from each prmtop. Hopefully the people that actually know these force
fields better can quickly compare these frcmod files to make sure they look
appropriate.

Hope this helps,
Jason

On Sun, Mar 27, 2011 at 4:39 AM, case <case.biomaps.rutgers.edu> wrote:

> Hi everyone:
>
> I have posted a new release candidate here:
>
> http://ambermd.org/downloads/AmberTools.26mar11.tar.bz2
>
> Still needed:
>
> 1. Proofreading of Users' Manual.
> 2. Testing of the ff10 force field files
> 3. Minor tweaks to the tests, esp. MMPBSA.py
>
> I know lots of people are at ACS, but any help you can give (especially for
> item 2) would help us get this baby out the door.
>
> ...thanks...dac
>
>
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
>



-- 
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032



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Received on Sun Mar 27 2011 - 13:00:04 PDT
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