Dear Carlos,
I am following closely this discussion about the incompatibilities
between ff03 and the other amber force field versions. So, first I would
like to ask you, what do you actually mean by "imbalance in elecrostatics".
Furthermore, the paper describing the ff03 speaks of correlation between
the "new" charges and the old charges and claims that at least in cases
of ligand-protein interactions, there should be no reason not to use
"old" ligand charges with "new" charges for protein residues.
Moreover, when ff03 is loaded into Leap, only non-terminal amino acids
are loaded from the new library, while N-terminal and C-terminal AA are
loaded from the old 94 libraries. So, isnt that inconssistent? Or is it
believed that non-terminal residues are not that important?...
The reason for asking these questions, is because according to studies
that have been done in our group (not by me), ff03 seems to be by far
the best version if one is interested in lifetimes and stabilities of
secondary structural elements (ff99SB was not tested). Is there any
reference which compares ff99SB with ff03 in that respect?
Best wishes
vlad
Carlos Simmerling wrote:
> due to the different charge model, you will need to find parameters
> developed specifically for ff03. using other sets would result in
> imbalance in electrostatics between different groups and is not
> a good idea. On the other hand, ff94, ff96, ff99 and several other
> variants such as our lab's ff99SB and parameters from Garcia and
> Pande all use the same charge model and will work with any parameters
> developed for ff94.
>
> Zu Thur Yew wrote:
>
>> Hi,
>>
>> I would like ask if there are any pTHR parameters suitable for use
>> with ff03?
>>
>> I know there are parms developed in the same way as ff94/ff99...the
>> charges for normal THR in ff99 & ff03 seems quite different...
>>
>> has anyone any experience using these parms with ff03? Would problems
>> be expected if these parameters are used with ff03?
>>
>> Any advice would be most appreciated!
>>
>> Many Thanks,
>>
>> ZT
>>
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--
Dr. Vlad Cojocaru
EML Research gGmbH
Molecular and Cellular Modeling Group
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg, Germany
Phone: +49-6221-533266
Fax: +49-6221-533298
e-mail: Vlad.Cojocaru.eml-r.villa-bosch.de
http://projects.villa-bosch.de/mcm/people/cojocaru/
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Received on Sun Aug 06 2006 - 06:07:09 PDT
