Introduction

A quick view

General description with a general list of what can be done and a first example on whats a molecule.

Example

Download the files metenk.pdb and traj_metenk.xtc to run a short example with the Methionine-Enkephaline coming from the 1PLW pdb.

In [1]: from aqua import *

In [2]: metenk=msystem('metenk.pdb',verbose=True)
# System created from the file metenk.pdb :
# 6015  atoms
# 1490  residues
# 2  chains
# 1485  waters
# 0  ions

In [3]: idS=metenk.selection('atom.type S')

In [4]: print 'The atom',metenk.atom[idS[0]].info(),'has the internal index:', idS[0]
The atom SD-68/MET-5 has the internal index: 67

In [5]: metenk.info_trajs()
# No coordinates

In [6]: metenk.load_traj('traj_metenk.xtc',frame='ALL',verbose=True)
# 21 frames/models in traj 0

In [7]: for ii in metenk.traj[0].frame:
   ...:     print '# Step',ii.step,'(t='+str(ii.time)+')','SD-68/MET-5 at', ii.coors[idS[0]]
   ...:
Step 0 (t=0.0) SD-68/MET-5 at [ 19.8200016   12.90999985    19.6400013 ]
Step 5000 (t=10.0) SD-68/MET-5 at [ 19.87000084    13.27000046  19.44000053]
Step 10000 (t=20.0) SD-68/MET-5 at [ 20.09000015    12.96000004  18.93000031]
...

See also

msystem, atom , msystem.selection(), msystem.load_traj(), msystem.info_trajs(), traj, frame

Units

Aqua works with the following units no matter the input data.

• Length: Angstroms
• Angles: Degrees
• Time: Picoseconds

Periodic Box and Cell

Aqua sets the coordinates of a molecular system always in the

positive cuadrant. This way any atom is placed is found in {[0,Lx),[0,Ly),[0,Lz)}, where Lx, Ly and Lz are the dimensions of the cubic box. It implies that molecules can be split if they are over the box edges.

Aqua works with cubic boxes at the moment. Orthorombic cells with

angles different from 90 degrees are not supported yet.