Re: AMBER: "personality" of Amber force field

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

HI,
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 ?

Thanks

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:
>
>
>>Hi,
>>
>>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
>><http://wos02.isiknowledge.com/?SID=836GcD5p.@1BlLM9am6&Func=Abstract&doc=3/19>
>>JOURNAL OF COMPUTATIONAL CHEMISTRY 24 (1): 21-31 JAN 15 2003
>>
>>Cheers,
>>
>>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 <tsaih.ncifcrf.gov>
>>Reply-To: amber.scripps.edu
>>To: amber.scripps.edu
>>
>>
>>
>>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!
>>Thanks.
>>
>>Gavin
>>
>>
>
>
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-- 
                            Dr. Adrian E. Roitberg
                              Associate Professor
               Quantum Theory Project and Department of Chemistry
University of Florida                         PHONE 352 392-6972
P.O. Box 118435                               FAX   352 392-8722
Gainesville, FL 32611-8435                    Email adrian.qtp.ufl.edu
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Received on Fri Mar 18 2005 - 21:53:00 PST
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