Or use ioutfm=1 in your input file to create a netcdf trajectory. Then you
just have to choose amber netcdf, regardless of whether or not it has
periodic boundary conditions, etc. ;)
On Mon, Mar 28, 2011 at 6:37 AM, Mahmoud Soliman <mahmoudelkot.gmail.com>wrote:
>
> Dear guys,
> Thanks a lot, that solved the probelm
> Best wishes
> Mahmoud
>
> 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 [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
>
> _______________________________________________
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Mar 28 2011 - 09:00:04 PDT
