Re: AMBER: "personality" of Amber force field

From: Adrian E. Roitberg <>
Date: Fri, 18 Mar 2005 16:24:50 -0500

It would be useful to give us more details on the meaning of 'helix prone'.

What system is this ? who do you know it is not a helix all the way ?


Hui-Hsu Tsai wrote:
> Thanks. Yes, I read this paper before. It talked about ff94 and ff99.
> Does any one have experience or comment on the "personality" of ff02 and
> ff03? My test so far shows they are also strongly helix-prone.
> I do not have too much experience on Amber force fields.
> Could amber expert or experienced users give me some comments?
> Gavin
> On Fri, 18 Mar 2005, Asim Okur wrote:
>>Your observation about the parm99 force field has been reported couple
>>of years ago. For more information please refer to ...
>>Okur A, Strockbine B, Hornak V, Simmerling C
>>Using PC clusters to evaluate the transferability of molecular mechanics
>>force fields for proteins
>>Asim Okur
>>-------- Original Message --------
>>Subject: AMBER: "personality" of Amber force field
>>Date: Wed, 16 Mar 2005 11:01:00 -0500 (EST)
>>From: Hui-Hsu Tsai <>
>>Dear Amber community,
>>I am writing this email to ask your comments on the "personality" of
>>different amber force fields and GB models.
>>In my GB + amber99 FF simulations, I oberserved the peptides and
>>proteins are strongly helix-prone. Does any one has experience on
>>amber02 FF? Does amber02 FF work better for b-strand formation? which GB
>>model works better? any comment is welcome!
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                            Dr. Adrian E. Roitberg
                              Associate Professor
               Quantum Theory Project and Department of Chemistry
University of Florida                         PHONE 352 392-6972
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Received on Fri Mar 18 2005 - 21:53:00 PST
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