AMBER Archive (2004)

Subject: Re: Re: AMBER: why the enegy of native state of protein is high in GBSA calculation?

From: J. Zhang, Dr (
Date: Sat Jun 05 2004 - 20:25:20 CDT

Many thanks to Carlos Simmerling and David A. Case.

>you need to read the literature more. it is
>now generally accepted that ff99 has serious
>bias and you should not expect the native state
>of a protein with significant beta-sheet content
>to be lowest in energy. try one of the more recent
>force fields provided in AMBER 8.
>Okur, A., Strockbine, B., Hornak, V. and Simmerling, C., ˇ®Using PC Clusters
>to Evaluate the Transferability of Molecular Mechanics Force Fields for
>Proteinsˇ±, J. Comput. Chem., 24:21, 2003.
>----- Original Message -----
>From: "J. Zhang, Dr" <>
>To: <>
>Sent: Friday, June 04, 2004 5:21 AM
>Subject: AMBER: why the enegy of native state of protein is high in GBSA
>> Dear Amber users,
>> Sorry for that this letter is relatively long.
>> I encountered a strange problem in my GBSA run. I found
>> the potential and total energy of the native state
>> of protein CI2 is even higher than that of non-native
>> state. But this is not correct.
>> I made two runs at temperature 100K, one was started from
>> the NMR structure of the native state of protein CI2, the
>> other was started from a relative random structure (see
>> the attached pdb files). Minimizations have been made before
>> the MD runs. In the calculations, the ff99 force field
>> and AMBER7 is used.
>> The mdin files in two runs are the same:
>> ------------------------------------------
>> constant temperature GBSA run
>> &cntrl
>> imin=0, ntb=0, ntt=1, ntc=2, ntf=2, dt=0.002, cut=8.0,
>> igb=2, gbsa=1,
>> ntpr = 10, ntwr=10, ntwx=10, ntwe=10,
>> nstlim = 1000000,
>> temp0 = 100,
>> tempi = 100,
>> tautp = 0.1,
>> &end
>> END
>> ------------------------------------------
>> The obtained energies (from mden files) are given in
>> the attached JPG file. To compare the two trajectories,
>> I put the energies of two trajectories together in
>> each figure. Long time simulations have been made to
>> ensure equilibrium, but here I only show the results
>> of a short time.
>> I can be seen that the potential and total energy of
>> native state are even higher that that of non-native state!
>> But this is not correct. The starting structures of two
>> runs are compared to the finial structures, and they are
>> almost the same. That is, the structures did not change much.
>> Similar results have also been seen in temperature 300K.
>> Why? Is this due to some incorrect parameters in my mdin file,
>> or due to improper force field chosen? or sth else?
>> Thank you very much for your help.
>> Best Regards,
>> ---
>> J. Zhang, Dr,
>> Institute of Biophysics,
>> Nanjing University
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