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
_______________________________________________
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
Received on Mon Mar 28 2011 - 06:30:10 PDT
