Re: [AMBER] enzyme MD trajectory looks funny

From: Mahmoud Soliman <mahmoudelkot.gmail.com>
Date: Mon, 28 Mar 2011 15:34:35 +0200

   Thanks a lot, it solves the problem
   Best wishes
   Mahmoud

When determining file type in VMD Molecule File Browser try to use
"AMBER Coordinates with Periodic Box" option.

On Mon, Mar 28, 2011 at 5:10 PM, Mahmoud Soliman [1]<mahmoudelkot.gmail.com> wr
ote:

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

  [2][3]http://www.bath.ac.uk/person/812559

References

  1. [4]http://people.bath.ac.uk/mess20/
  2. [5]http://www.bath.ac.uk/person/812559

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AMBER mailing list
[6]AMBER.ambermd.org
[7]http://lists.ambermd.org/mailman/listinfo/amber




   --

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

   Mahmoud E. Soliman

   Computational Chemistry & Modeling (PhD)

   Department of Chemistry

   University of Bath

   Bath

   BA2 7AY

   United Kingdom

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

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


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

   Mahmoud E. Soliman

   Lecturer of pharmaceutical organic chemistry

   Pharmaceutical Organic Chemistry Dept.

   Faculty of pharmacy

   Zagazig University

   Zagazig

   Egypt

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

   Email:

   [10]mess20.bath.ac.uk

   [11]meelkot.zu.edu.eg

   [12]mahmoudelkot.gmail.com

References

   1. mailto:mahmoudelkot.gmail.com
   2. http://people.bath.ac.uk/mess20/
   3. http://www.bath.ac.uk/person/812559
   4. http://people.bath.ac.uk/mess20/
   5. http://www.bath.ac.uk/person/812559
   6. mailto:AMBER.ambermd.org
   7. http://lists.ambermd.org/mailman/listinfo/amber
   8. http://people.bath.ac.uk/mess20/
   9. http://www.bath.ac.uk/person/812559
  10. mailto:mess20.bath.ac.uk
  11. mailto:meelkot.zu.edu.eg
  12. mailto:mahmoudelkot.gmail.com
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Received on Mon Mar 28 2011 - 06:30:10 PDT
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