AMBER Archive (2005)

Subject: Re:AMBER: "personality" of Amber force field

From: Asim Okur (aokur_at_ic.sunysb.edu)
Date: Fri Mar 18 2005 - 15:01:19 CST

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_at_ncifcrf.gov>
Reply-To: amber_at_scripps.edu
To: amber_at_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 

-- 
Asim Okur
Stony Brook University
Chemistry Department
Stony Brook, NY 11794-3400
631 - 632 1560

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu