[AMBER] enzyme MD trajectory looks funny

From: Mahmoud Soliman <mahmoudelkot.gmail.com>
Date: Mon, 28 Mar 2011 15:10:38 +0200

   Dear Amber experts,
   I am running a QM/MM/MD simulation for an enzyme-ligand complex in a TIB3P
   box. The output file looks fine, the energies look ok and it terminates
   successfully, however, when I visualize the trajectory using VMD I see that
   after the first frame all atoms (solute and waters) appear to be connected
   and the whole thing seems weird. Attached two pictures, one showing the
   first frame and the other showing the second frame....Below is my input
   file. This only happens to me when I do explicit solvent box (classical or
   QM/MM simulation)..Any idea what is going wrong? I could email a piece of
   the trajectory file as well as the pdb of the starting structure to whoever
   can help me! for your information, my starting PDB structure was optimized
   at QM/MM level and optimization went fine!

   QM/MM equilibration with some restraints

   &cntrl

   imin = 0,

   irest = 0,

   ntx = 1,

   ntb = 1,

   taup = 2,

   cut = 10,

   tempi = 100.0, temp0 = 300.0,

   ntc=2,

   ntf=2,

   ntt = 3,

   tol = 0.0001,

   iwrap = 1,

   ntt = 3,

   gamma_ln = 1.0,

   scee= 1.2,

   nstlim =50000, dt = 0.002,

   ntpr = 500, ntwx = 500, ntwr = 500, ntwe = 500,

   ntr = 1, restraint_wt=2.0, restraintmask=':1-186',

   ifqnt=1

   /

   &qmmm

   iqmatoms=
   1132,1133,1134,1135,1136,1137,2582,2583,2584,2585,2586,2587,2588,2772,2773,2
   774,2775,2776,2777,2778,2779,2780,2781,2782,2783,2784,2785,2786,2787,2788,27
   89,2790,2791,2792,2793,2794,2795,2796,2797,2798,2799,2800,2801,2802,2803,280
   4,2805,2806,2807,2808,2809,2810,2811,2812,2813,2814,2815,2816,2817,2818,2819
   ,

   qmcharge=-1,

   qm_theory='AM1',

   qmcut=8.0,

   writepdb=1

   qmshake=0,

   /
   Thanks
   Mahmoud

   *************************************************

   Mahmoud E. Soliman

   Computational Chemistry & Modeling (PhD)

   Department of Chemistry

   University of Bath

   Bath

   BA2 7AY

   United Kingdom

   [1]http://people.bath.ac.uk/mess20/

   [2]http://www.bath.ac.uk/person/812559

References

   1. http://people.bath.ac.uk/mess20/
   2. http://www.bath.ac.uk/person/812559


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Received on Mon Mar 28 2011 - 06:30:04 PDT
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