Francesco's paper cites the work of Piana et al (ref 50) when mentioning
ff99sb-ildn** in the Materials and Methods ...
http://www.sciencedirect.com/science/article/pii/S0006349511004097
However I do not see anything about a new adaptation (**) in this
particular paper .... So, the extra * in Franceso's paper might just be
a typo or the reference 50 is misplaced .... I am actually not aware of
any plublished further modification of the ff99sb-ildn*
But sure I might have missed something .... So, please correct me if I
am wrong ...
Vlad
On 07/14/2016 01:40 PM, Thomas Evangelidis wrote:
>
>
>
>
>
>> 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.
>
>
>
>
--
Dr. Vlad Cojocaru
Computational Structural Biology Laboratory
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]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/43241/cojocaru
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Received on Thu Jul 14 2016 - 05:00:04 PDT
