> At that time, Francesco Gervasio sent me his implementation of the
> ff99sb-ildn* force field in Amber but we could not use it because of
> some atom type incompatibilites (if I recall correctly, it was long ago)
> ....
>
> In the meantime we switched to the ff14SB (which is now published).
> However, some recent posts indicated some potential issues with the chi
> dihedrals in aromatic residues which apparently do not appear in ff12SB
> (its predecessor) ...
>
> So, my advice would be: unless you really depend on that particular
> force field, switch to what is available in Amber. There is probably no
> "one best force field" out there and you may find issue with any of them
> .... But using what is available in Amber for simulations with Amber
> topology is safer than conversions and adaptations.
>
> If you do insist on using ff99sb-ildn*, try to email
>
> Francesco Gervasio
> and maybe you can adapt his implementation ....
>
I haven't followed updates in the protein force fields for quite a while,
but as far as I remember, Francesco Gervasio made some corrections to the
charged residues to reproduce more accurately the strength of salt-bridges.
http://pubs.acs.org/doi/abs/10.1021/jp500958r
He named the force field AMBER99SB**-ILDN as stated in this publication:
http://journals.plos.org/ploscompbiol/article/asset?unique&id=info:doi
/10.1371/journal.pcbi.1003863.s009
I am not sure if these corrections are included in his AMBER
implementation. Maybe you should point this out if you ask him for the
files.
--
======================================================================
Thomas Evangelidis
Research Specialist
CEITEC - Central European Institute of Technology
Masaryk University
Kamenice 5/A35/1S081,
62500 Brno, Czech Republic
email: tevang.pharm.uoa.gr
tevang3.gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Thu Jul 14 2016 - 05:00:03 PDT
