Just try to load ur trajectory as "AMBER coordinates with periodic box" *file
type* in the VMD Molecule file browser dialogue box
Regards
Rajeswari. A
On Mon, Mar 28, 2011 at 6:37 PM, Per Jr. Greisen <pgreisen.gmail.com> wrote:
> have you loaded with periodic boundary conditions? Furthermore you
> might want to reimage your trajectory(it is explained in the tutorial
> or in the documentation of ambertools how to re-image a trajectory).
>
> Hope this helps
>
> On Mon, Mar 28, 2011 at 3:10 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
> >
> >
>
>
>
> --
> Per
>
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Received on Mon Mar 28 2011 - 06:30:07 PDT
