Re: [AMBER] Query regarding the ff99SB*ildn force field

From: Vlad Cojocaru <>
Date: Wed, 31 Jan 2018 14:55:45 +0100

I believe Francesco Gervasio has developed at some point the files
needed to use that force field in Amber. ... However, I recall from my
initial attempts to use those files that they are incompatible with
newer Amber versions because of atom type overlaps with newer Amber
force fields .... So, even if you get the files from Francesco, I guess
some work to adapt them to the newest Amber may be required .... Anyhow,
in such cases please be very careful and make sure you will be using the
correct parameters (e.g. by specific tests on your topology using parmed
or other tools).

I'd be curious to know why are you particularly interested in using that
force filed for simulations of unstructured proteins ? ... I am not an
expert in such simulations, but as far I recall from a review by Piana
et al (Curr Opin Struct Biol 2014), the force field was not very good at
describing the unfolded ensemble in protein folding simulations ....This
may mean that its not that good with unstructured proteins either.
Having said this, I believe some good agreement with NMR data was shown
in a JACS paper 2012 by Lindorff-Larsen et al ... You may want to check
more recent progress in the development of force fields for unstructured
proteins ....

But perhaps I am missing some details .... So, it would be nice to know
the arguments for this force field ....


On 01/31/2018 02:32 PM, David A Case wrote:
> On Wed, Jan 31, 2018, Leena Aggarwal wrote:
>> I am working with intrinsically disordered proteins and I want to use
>> ff99SB*ildn force field. In Amber 12, I was able to use ff99SBildn force
>> field but I was not able to use ff99SB*ildn force field.
> It is still true that we don't distribute files for ff99SB*ildn.
> We do (as you have found) have files for ff99SBildn. If ff99SB*ildn is
> a fairly small change, perhaps someone could make the required modifications.
> Or maybe someone has already done that, and would be willing to share.
> ....dac
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> AMBER mailing list

Vlad Cojocaru, PD (Habil.), Ph.D.
Project Group Leader
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]
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Received on Wed Jan 31 2018 - 06:00:06 PST
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