Messages

1

MD simulations / Base pair number not staying constant in simulations

« on: May 21, 2025, 08:16:27 am »

Hi all,

I have managed to briefly analyze my simulations with dnaMD Python module. I managed to analyze the curvature of the unbound DNA but I ran into issues while analyzing the bound DNA.

The 3DNA calculations finish fine, but they identify different number of base pairs in different frames. There are 40 base pairs in the starting structure, but in some frames this drops to 35.

I can load the helical axis with step range defined:

complexdna.set_helical_axis('complex2/HelAxis_complex2_test.dat',step_range=True, step=[10,25])

But I can't continue the curvature analysis, because the command

complexdna.generate_smooth_axis(step_range=True, step=[10,25], smooth=500, spline=2, fill_point=6, cut_off_angle=180)

Leads to an error (which happens around the time when the base pair number goes very low):

Fitting spline curve on helical axis of frame 6000 out of 80000 frames
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Cell In[24], line 2
      1 # Generate global axis by interpolation (smoothening)
----> 2 complexdna.generate_smooth_axis(step_range=True, step=[10,25], smooth=500, spline=2, fill_point=6, cut_off_angle=180)
      4 # Calculate curvature and tangent along global helical axis
      5 #freedna.calculate_curvature_tangent(store_tangent=True)

File ~/.local/lib/python3.9/site-packages/dnaMD/dnaMD.py:1322, in DNA.generate_smooth_axis(self, step_range, step, smooth, spline, fill_point, cut_off_angle)
   1318     sys.stdout.write("\rFitting spline curve on helical axis of frame %d out of %d frames" % (
   1319         frame_number, nframes))
   1320     sys.stdout.flush()
-> 1322 xsmooth, ysmooth, zsmooth, mask = fit_axis(bp_idx, frame_number, RawX, RawY, RawZ, smooth, spline, fill_point, cut_off_angle)
   1323 maskArray = mask
   1325 smoothX.append(xsmooth)

File ~/.local/lib/python3.9/site-packages/dnaMD/dnaMD.py:2621, in fit_axis(bp_idx, nframe, RawX, RawY, RawZ, smooth, spline, fill_point, cut_off_angle)
   2618 points = fill_point * len(orig_x)
   2620 nest = -1
-> 2621 tckp, u = splprep([orig_x, orig_y, orig_z], s=smooth, k=spline, nest=nest)
   2623 xnew, ynew, znew = splev(np.linspace(0, 1, points), tckp)
   2625 new_axis = np.array([xnew, ynew, znew]).T

File /usr/local/lib/python3.9/site-packages/scipy/interpolate/_fitpack_py.py:155, in splprep(x, w, u, ub, ue, k, task, s, t, full_output, nest, per, quiet)
     13 def splprep(x, w=None, u=None, ub=None, ue=None, k=3, task=0, s=None, t=None,
     14             full_output=0, nest=None, per=0, quiet=1):
     15     """
     16     Find the B-spline representation of an N-D curve.
     17
   (...)
    152
    153     """
--> 155     res = _impl.splprep(x, w, u, ub, ue, k, task, s, t, full_output, nest, per,
    156                         quiet)
    157     return res

File /usr/local/lib/python3.9/site-packages/scipy/interpolate/_fitpack_impl.py:175, in splprep(x, w, u, ub, ue, k, task, s, t, full_output, nest, per, quiet)
    173 wrk = _parcur_cache['wrk']
    174 iwrk = _parcur_cache['iwrk']
--> 175 t, c, o = _fitpack._parcur(ravel(transpose(x)), w, u, ub, ue, k,
    176                            task, ipar, s, t, nest, wrk, iwrk, per)
    177 _parcur_cache['u'] = o['u']
    178 _parcur_cache['ub'] = o['ub']

ValueError: Invalid inputs.

Also the 3DNA HelAxis*.dat files contained ---- for some base pairs which were not understood by dnaMD. I needed to replace them with 0.00 to get the file read.

Could you help me get the curvature analyzed also for the bound DNA? I only used the DNA atoms in the analyzed bound trajectory to get a comparison with the unbound DNA.

If needed, I can share some files for testing.

2

MD simulations / Re: Do I need gromacs to use dnaMD for simulations?

« on: May 20, 2025, 03:20:40 am »

Thanks for the help!

Now I have managed to install both 3DNA and do_x3DNA for GROMACS. However, it seems do_x3DNA needs 'residuetypes.dat' file form GROMACS installation. It seems I was able to bypass this by downloading the file form github and putting it in the working folder. I thought you might want to put a note of this to the documentation.

Keep up the good work!

3

MD simulations / Do I need gromacs to use dnaMD for simulations?

« on: May 16, 2025, 05:50:16 am »

Hi all,

Thanks for the x3DNA-DSSR software which works wonderfully for single PDBs.

I have some MD simulations I would like to analyze with dnaMD. I ran them with Amber but converted them to GROMACS .xtc + .pdb files for analysis.

Do I need GROMACS version of dnaMD to analyze simulations or can I use the Python module of dnaMD without GROMACS for simulations?

PS. I am also lacking the link to download the 3DNA from the forum for some reason, my forum view is similar to unregistered users.