Re: [AMBER] enzyme MD trajectory looks funny

From: Dmitry Nilov <nilovdm.gmail.com>
Date: Mon, 28 Mar 2011 17:20:53 +0400

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 <mahmoudelkot.gmail.com> wrote:
>
>   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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>



-- 
Dmitry Nilov,
Faculty of Bioengineering and Bioinformatics,
Lomonosov Moscow State University
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Mar 28 2011 - 06:30:09 PDT
Custom Search