[AMBER] Deformed structures

From: Damiano Spadoni <enxds6.nottingham.ac.uk>
Date: Wed, 25 Nov 2015 16:23:29 +0000

Dear AMBERs,

I am try to run the heating step of a protein containing pyridoxal phosphate as cofactor.

I initially run this stage applying NMR restraints for the metallic cluster buried in it and restraintmask for the pyridoxal cofactor. As the mentioned pyridoxal structures appeared deformed, the restraints have been dropped thinking that they might be the cause of such a deformation.

Even with no restraints at all and running the heating carefully (0 - 50K, dt = 0.0001) the problem persists.
I am wondering if anyone of you have encountered this problem before and what else may be the cause and, obviously, the solution.

This is my last input file:
imin = 0,
  irest = 0,
  ntx = 1,
  ntb = 1,
  cut = 10.0,
  ntc = 2,
  ntf = 2,
  tempi = 0.0,
  temp0 = 50.0,
  ntt = 3,
  ig = -1, gamma_ln = 1.0,
  nstlim = 10000, dt = 0.0001,
  ntpr = 10, ntwx = 10, ntwr = 10,
  ntr = 0,
  nmropt = 0, vlimit = 5.0


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Received on Wed Nov 25 2015 - 08:30:04 PST
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