Cannot read dcd file from MDAnalysis in CHARMM

[uroehrig]

Hi,

I'm trying to write a trajectory dcd file (20 frames) with CHARMM, read it with MDAnalysis (eventually select some frames), write it with MDAnalysis and read it back with CHARMM.

My python code looks simply like this:

u = Universe('relax0.psf','relax0.dcd', in_memory=True)
u.atoms.write('tmp.dcd', frames='all')

When I try to read the trajectory back in CHARMM, reading tmp.dcd instead of relax0.dcd, CHARMM is only able to read the first frame, then it exits with

  ***** LEVEL -1 WARNING FROM <REATRJ> *****
  ***** INPUT TRAJECTORY NOT SET UP.
  ******************************************

When reading the first frame of tmp.dcd, CHARMM prints the following:
NUMBER OF COORDINATE SETS IN FILE: 20
NUMBER OF PREVIOUS DYNAMICS STEPS: 0
FREQUENCY FOR SAVING COORDINATES: 1
NUMBER OF STEPS FOR CREATION RUN: 0

While with the original file relax0.dcd , CHARMM prints the following:
NUMBER OF COORDINATE SETS IN FILE: 20
NUMBER OF PREVIOUS DYNAMICS STEPS: 1
FREQUENCY FOR SAVING COORDINATES: 1
NUMBER OF STEPS FOR CREATION RUN: 20

Do you have any suggestion on how to get a CHARMM-compatible dcd file?

Thank you in advance for your help,
Ute

[uroehrig]

I found a way to read a trajectory dcd file created by MDAnalysis in CHARMM. I'm posting it, as it may be helpful for others.

Indicating the first and the last frame, the dcd file can be read. For example, if the dcd file has 20 frames:

OPEN READ UNIT 10 FILE NAME mda-writte-file.dcd
TRAJ IREAD 10 NUNIT 1 BEGIN 0 STOP 19

All the best,
Ute