AMBER Archive (2008)

Subject: AMBER: aromatic residues lost planarity during MD simulation

From: cniu_at_ualberta.ca
Date: Mon Apr 21 2008 - 15:18:26 CDT

Dear all,
I am running an md simulation using Amber9. After energy minimization
and restrained dynamics (increasing the system temperature from Ok to
300K), I performed equilibration for 200ps and I found all the
aromatic rings (in Phe, Tyr, His, etc) have lost their planarity. That
sounds unreasonable but I cannot figure out what's wrong with my input
file. I used leaprc.ff99 and my md input file follows,

  &cntrl
   imin = 0,
   ntx = 7, irest = 1,
   ntb = 2, pres0 =1.0, ntp = 1,
   taup = 2,
   ntr = 0,
   cut = 10,
   ntc = 2, ntf = 2,
   tempi = 300.0, temp0 = 300.0,
   ntt = 3,
   gamma_ln = 1.0,
   nstlim = 100000, dt = 0.002,
   ntpr = 100, ntwx = 500, ntwr = 1000
  /
END

Thanks in advance to anyone that will give any suggestion.

Amara

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