AMBER Archive (2008)

Subject: AMBER: ff94 vs. ff03

From: Swarup Gupta (
Date: Fri May 23 2008 - 19:26:46 CDT

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 experimental.
  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 MMGBSA?

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