AMBER Archive (2008)

Subject: RE: AMBER: ff94 vs. ff03

From: Ross Walker (
Date: Fri May 23 2008 - 21:58:45 CDT

Hi Swarup


The charge fitting procedure in FF03 is very different from FF94. It may be
that there are issues with FF03 and GB - I don't know how extensively this
has been tried, maybe others could comment more here. You could try FF99SB
this corrects most of the problems with FF94 but does not change the
underlying charge model.


There is also of the course the possibility that the original results were
just a very fortuitous cancellation of errors. I.e. the use of GB skews
things one way while the FF94 issues skew it the other way and you just
happen to end up in the middle.


Good luck,



From: [] On Behalf Of
Swarup Gupta
Sent: Friday, May 23, 2008 5:27 PM
Subject: AMBER: ff94 vs. ff03


I am trying to benchmark a protin-protein binding energy data. First it runs
explicit water MD and then it is postprocessed by MMGBSA method and NMA .


There are some published data in the literature on the same system using
ff94 (and same protocol mentioned above) which is in the range of
experimental data. I can closely reporoduce the data if I use ff94. But If I
use ff03 then I get an over stabilization of 10kcal/mol than that I get
from ff94. This is in enthalpy part. But NMA is OK.


Overstabilization is leading to very high binding energy, far away from


I am uning the default input parametetrs (igb=2 and zero salt concentration)
for MMGBSA scripts provided with the AMBER package.


Is there anything which is fundamentally different in ff03 that may lead to
this difference of delH or I should use a different input parameter set for





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